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Turtle L, Elliot S, Drake TM, Thorpe M, Khoury EG, Greenhalf W, Hardwick HE, Leeming G, Law A, Oosthuyzen W, Pius R, Shaw CA, Baillie JK, Openshaw PJM, Docherty AB, Semple MG, Harrison EM, Palmieri C. Changes in hospital mortality in patients with cancer during the COVID-19 pandemic (ISARIC-CCP-UK): a prospective, multicentre cohort study. Lancet Oncol 2024:S1470-2045(24)00107-4. [PMID: 38621404 DOI: 10.1016/s1470-2045(24)00107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Patients with cancer are at greater risk of dying from COVID-19 than many other patient groups. However, how this risk evolved during the pandemic remains unclear. We aimed to determine, on the basis of the UK national pandemic protocol, how factors influencing hospital mortality from COVID-19 could differentially affect patients undergoing cancer treatment. We also examined changes in hospital mortality and escalation of care in patients on cancer treatment during the first 2 years of the COVID-19 pandemic in the UK. METHODS We conducted a prospective cohort study of patients aged older than 19 years and admitted to 306 health-care facilities in the UK with confirmed SARS-CoV-2 infection, who were enrolled in the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol (CCP) across the UK from April 23, 2020, to Feb 28, 2022; this analysis included all patients in the complete dataset when the study closed. The primary outcome was 30-day in-hospital mortality, comparing patients on cancer treatment and those without cancer. The study was approved by the South Central-Oxford C Research Ethics Committee in England (Ref: 13/SC/0149) and the Scotland A Research Ethics Committee (Ref 20/SS/0028), and is registered on the ISRCTN Registry (ISRCTN66726260). FINDINGS 177 871 eligible adult patients either with no history of cancer (n=171 303) or on cancer treatment (n=6568) were enrolled; 93 205 (52·4%) were male, 84 418 (47·5%) were female, and in 248 (13·9%) sex or gender details were not specified or data were missing. Patients were followed up for a median of 13 (IQR 6-21) days. Of the 6568 patients receiving cancer treatment, 2080 (31·7%) died at 30 days, compared with 30 901 (18·0%) of 171 303 patients without cancer. Patients aged younger than 50 years on cancer treatment had the highest age-adjusted relative risk (hazard ratio [HR] 5·2 [95% CI 4·0-6·6], p<0·0001; vs 50-69 years 2·4 [2·2-2·6], p<0·0001; 70-79 years 1·8 [1·6-2·0], p<0·0001; and >80 years 1·5 [1·3-1·6], p<0·0001) but a lower absolute risk (51 [6·7%] of 763 patients <50 years died compared with 459 [30·2%] of 1522 patients aged >80 years). In-hospital mortality decreased for all patients during the pandemic but was higher for patients on cancer treatment than for those without cancer throughout the study period. INTERPRETATION People with cancer have a higher risk of mortality from COVID-19 than those without cancer. Patients younger than 50 years with cancer treatment have the highest relative risk of death. Continued action is needed to mitigate the poor outcomes in patients with cancer, such as through optimising vaccination, long-acting passive immunisation, and early access to therapeutics. These findings underscore the importance of the ISARIC-WHO pandemic preparedness initiative. FUNDING National Institute for Health Research and the Medical Research Council.
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Affiliation(s)
- Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Sarah Elliot
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK
| | - Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK
| | - Mathew Thorpe
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK
| | - Emma G Khoury
- Academic Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - William Greenhalf
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Hayley E Hardwick
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Gary Leeming
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Andy Law
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, UK
| | - Riinu Pius
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK
| | - Catherine A Shaw
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK
| | - J Kenneth Baillie
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, UK; Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | | | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK
| | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK.
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Michael BD, Dunai C, Needham EJ, Tharmaratnam K, Williams R, Huang Y, Boardman SA, Clark JJ, Sharma P, Subramaniam K, Wood GK, Collie C, Digby R, Ren A, Norton E, Leibowitz M, Ebrahimi S, Fower A, Fox H, Tato E, Ellul MA, Sunderland G, Held M, Hetherington C, Egbe FN, Palmos A, Stirrups K, Grundmann A, Chiollaz AC, Sanchez JC, Stewart JP, Griffiths M, Solomon T, Breen G, Coles AJ, Kingston N, Bradley JR, Chinnery PF, Cavanagh J, Irani SR, Vincent A, Baillie JK, Openshaw PJ, Semple MG, Taams LS, Menon DK. Author Correction: Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses. Nat Commun 2024; 15:2918. [PMID: 38575615 PMCID: PMC10995197 DOI: 10.1038/s41467-024-47320-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Affiliation(s)
- Benedict D Michael
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK.
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK.
- The Walton Centre NHS Foundation Trust, Liverpool, L9 7BB, UK.
| | - Cordelia Dunai
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK
| | - Edward J Needham
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kukatharmini Tharmaratnam
- Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, L69 3GF, UK
| | - Robyn Williams
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Departments of Neurology and Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yun Huang
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Sarah A Boardman
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Jordan J Clark
- University of Liverpool, Liverpool, L69 7BE, UK
- Department of Microbiology, Icahn School of Medicine, Mount Sinai, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine, Mount Sinai, NY, 10029, USA
| | - Parul Sharma
- Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Krishanthi Subramaniam
- Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Greta K Wood
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Ceryce Collie
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Richard Digby
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Alexander Ren
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Emma Norton
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Maya Leibowitz
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Soraya Ebrahimi
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Andrew Fower
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah Fox
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Esteban Tato
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
- NIHR Maudsley Biomedical Research Centre, King's College London, London, SE5 8AF, UK
| | - Mark A Ellul
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- The Walton Centre NHS Foundation Trust, Liverpool, L9 7BB, UK
| | - Geraint Sunderland
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Marie Held
- Centre for Cell Imaging, Liverpool Shared Research Facilities, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Claire Hetherington
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Franklyn N Egbe
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Alish Palmos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
- NIHR Maudsley Biomedical Research Centre, King's College London, London, SE5 8AF, UK
| | - Kathy Stirrups
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Alexander Grundmann
- Clinical Neurosciences, Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, SO17 1BF, UK
- Department of Neurology, Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Anne-Cecile Chiollaz
- Département de médecine interne des spécialités (DEMED), University of Geneva, Geneva, CH-1211, Switzerland
| | - Jean-Charles Sanchez
- Département de médecine interne des spécialités (DEMED), University of Geneva, Geneva, CH-1211, Switzerland
| | - James P Stewart
- Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Michael Griffiths
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Tom Solomon
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK
- The Walton Centre NHS Foundation Trust, Liverpool, L9 7BB, UK
- The Pandemic Institute, Liverpool, L7 3FA, UK
| | - Gerome Breen
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
- NIHR Maudsley Biomedical Research Centre, King's College London, London, SE5 8AF, UK
| | - Alasdair J Coles
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge, CB2 0QQ, UK
| | - John R Bradley
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
| | - Jonathan Cavanagh
- Centre for Immunology, School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Departments of Neurology and Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Angela Vincent
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Peter J Openshaw
- National Heart and Lung Institute, Imperial College London, London, SW7 2BX, UK
- Imperial College Healthcare NHS Trust, London, W2 1NY, UK
| | - Malcolm G Semple
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK
- Respiratory Unit, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, L14 5AB, UK
| | - Leonie S Taams
- Centre for Inflammation Biology and Cancer Immunology, King's College London, London, SE1 9RT, UK
| | - David K Menon
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
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Devine K, Russell CD, Blanco GR, Walker BR, Homer NZM, Denham SG, Simpson JP, Leavy OC, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Greening NJ, Lone NI, Thorpe M, Greenhalf W, Chalmers JD, Ho LP, Horsley A, Marks M, Raman B, Moore SC, Dunning J, Semple MG, Andrew R, Wain LV, Evans RA, Brightling CE, Kenneth Baillie J, Reynolds RM. Plasma steroid concentrations reflect acute disease severity and normalise during recovery in people hospitalised with COVID-19. Clin Endocrinol (Oxf) 2024; 100:317-327. [PMID: 38229583 DOI: 10.1111/cen.15012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024]
Abstract
OBJECTIVE Endocrine systems are disrupted in acute illness, and symptoms reported following coronavirus disease 2019 (COVID-19) are similar to those found with clinical hormone deficiencies. We hypothesised that people with severe acute COVID-19 and with post-COVID symptoms have glucocorticoid and sex hormone deficiencies. DESIGN/PATIENTS Samples were obtained for analysis from two UK multicentre cohorts during hospitalisation with COVID-19 (International Severe Acute Respiratory Infection Consortium/World Health Organisation [WHO] Clinical Characterization Protocol for Severe Emerging Infections in the UK study), and at follow-up 5 months after hospitalisation (Post-hospitalisation COVID-19 study). MEASUREMENTS Plasma steroids were quantified by liquid chromatography-mass spectrometry. Steroid concentrations were compared against disease severity (WHO ordinal scale) and validated symptom scores. Data are presented as geometric mean (SD). RESULTS In the acute cohort (n = 239, 66.5% male), plasma cortisol concentration increased with disease severity (cortisol 753.3 [1.6] vs. 429.2 [1.7] nmol/L in fatal vs. least severe, p < .001). In males, testosterone concentrations decreased with severity (testosterone 1.2 [2.2] vs. 6.9 [1.9] nmol/L in fatal vs. least severe, p < .001). In the follow-up cohort (n = 198, 62.1% male, 68.9% ongoing symptoms, 165 [121-192] days postdischarge), plasma cortisol concentrations (275.6 [1.5] nmol/L) did not differ with in-hospital severity, perception of recovery, or patient-reported symptoms. Male testosterone concentrations (12.6 [1.5] nmol/L) were not related to in-hospital severity, perception of recovery or symptom scores. CONCLUSIONS Circulating glucocorticoids in patients hospitalised with COVID-19 reflect acute illness, with a marked rise in cortisol and fall in male testosterone. These findings are not observed 5 months from discharge. The lack of association between hormone concentrations and common post-COVID symptoms suggests steroid insufficiency does not play a causal role in this condition.
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Affiliation(s)
- Kerri Devine
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, UK
| | - Giovanny R Blanco
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Brian R Walker
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Natalie Z M Homer
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Scott G Denham
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Joanna P Simpson
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Olivia C Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Omer Elneima
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Hamish J C McAuley
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Aarti Shikotra
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Amisha Singapuri
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Marco Sereno
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ruth M Saunders
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Victoria C Harris
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | | | - Neil J Greening
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Nazir I Lone
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Mathew Thorpe
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - James D Chalmers
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | - Alex Horsley
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Michael Marks
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Hospital for Tropical Diseases, University College London Hospital, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Betty Raman
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Jake Dunning
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Ruth Andrew
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Rachael A Evans
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | | | - John Kenneth Baillie
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rebecca M Reynolds
- BHF/University Centre for Cardiovascular Science, Queen's Medical Research Institute, Edinburgh Bioquarter, University of Edinburgh, Edinburgh, UK
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Liew F, Efstathiou C, Fontanella S, Richardson M, Saunders R, Swieboda D, Sidhu JK, Ascough S, Moore SC, Mohamed N, Nunag J, King C, Leavy OC, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Harris VC, Houchen-Wolloff L, Greening NJ, Lone NI, Thorpe M, Thompson AAR, Rowland-Jones SL, Docherty AB, Chalmers JD, Ho LP, Horsley A, Raman B, Poinasamy K, Marks M, Kon OM, Howard LS, Wootton DG, Quint JK, de Silva TI, Ho A, Chiu C, Harrison EM, Greenhalf W, Baillie JK, Semple MG, Turtle L, Evans RA, Wain LV, Brightling C, Thwaites RS, Openshaw PJM. Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease. Nat Immunol 2024; 25:607-621. [PMID: 38589621 PMCID: PMC11003868 DOI: 10.1038/s41590-024-01778-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/06/2024] [Indexed: 04/10/2024]
Abstract
One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood1. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.
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Affiliation(s)
- Felicity Liew
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Matthew Richardson
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ruth Saunders
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dawid Swieboda
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jasmin K Sidhu
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Stephanie Ascough
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Noura Mohamed
- The Imperial Clinical Respiratory Research Unit, Imperial College NHS Trust, London, UK
| | - Jose Nunag
- Cardiovascular Research Team, Imperial College Healthcare NHS Trust, London, UK
| | - Clara King
- Cardiovascular Research Team, Imperial College Healthcare NHS Trust, London, UK
| | - Olivia C Leavy
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Omer Elneima
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Hamish J C McAuley
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Aarti Shikotra
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Amisha Singapuri
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Marco Sereno
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Victoria C Harris
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Linzy Houchen-Wolloff
- Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK
| | - Neil J Greening
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Nazir I Lone
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Matthew Thorpe
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - A A Roger Thompson
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Sarah L Rowland-Jones
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - James D Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | - Alexander Horsley
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Betty Raman
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Michael Marks
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Hospital for Tropical Diseases, University College London Hospital, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Onn Min Kon
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Luke S Howard
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Daniel G Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jennifer K Quint
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Antonia Ho
- MRC Centre for Virus Research, School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Christopher Chiu
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - William Greenhalf
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - J Kenneth Baillie
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Pandemic Science Hub, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- The Pandemic Institute, University of Liverpool, Liverpool, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- The Pandemic Institute, University of Liverpool, Liverpool, UK
| | - Rachael A Evans
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Louise V Wain
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Christopher Brightling
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK.
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Alrezaihi A, Penrice-Randal R, Dong X, Prince T, Randle N, Semple MG, Openshaw PJM, MacGill T, Myers T, Orr R, Zakotnik S, Suljič A, Avšič-Županc T, Petrovec M, Korva M, AlJabr W, Hiscox JA. Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome. J Clin Virol 2024; 171:105620. [PMID: 38237303 DOI: 10.1016/j.jcv.2023.105620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/06/2023] [Accepted: 11/18/2023] [Indexed: 03/17/2024]
Abstract
Simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample would help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. However, given the large sequence background, unenriched metatranscriptomic approaches often do not sequence SARS-CoV-2 to sufficient read and coverage depth to obtain a consensus genome, especially with moderate and low viral loads from clinical samples. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected seasonal coronaviruses. The feasibility of profiling the nasal microbiome using these enrichment methods was explored. The findings shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome.
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Affiliation(s)
| | | | | | | | | | - Malcolm G Semple
- University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK; Alder Hey Children's Hospital, Liverpool, UK
| | | | - Tracy MacGill
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | - Todd Myers
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | - Robert Orr
- Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, USA
| | | | - Alen Suljič
- University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Miša Korva
- University of Ljubljana, Ljubljana, Slovenia
| | - Waleed AlJabr
- University of Liverpool, Liverpool, UK; King Fahad Medical City, Riyadh, Saudi Arabia
| | - Julian A Hiscox
- University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK; Agency for Science, Technology and Research (A*STAR), Singapore.
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6
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Cho SM, Premraj L, Battaglini D, Fanning JP, Suen J, Bassi GL, Fraser J, Robba C, Griffee M, Solomon T, Semple MG, Baillie K, Sigfrid L, Scott JT, Citarella BW, Merson L, Arora RC, Whitman G, Thomson D, White N. Sex differences in post-acute neurological sequelae of SARS-CoV-2 and symptom resolution in adults after coronavirus disease 2019 hospitalization: an international multi-centre prospective observational study. Brain Commun 2024; 6:fcae036. [PMID: 38444907 PMCID: PMC10914448 DOI: 10.1093/braincomms/fcae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/11/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Although it is known that coronavirus disease 2019 can present with a range of neurological manifestations and in-hospital complications, sparse data exist on whether these initial neurological symptoms of coronavirus disease 2019 are closely associated with post-acute neurological sequelae of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2; PANSC) and whether female versus male sex impacts symptom resolution. In this international, multi-centre, prospective, observational study across 407 sites from 15 countries (30 January 2020 to 30 April 2022), we report the prevalence and risk factors of PANSC among hospitalized adults and investigate the differences between males and females on neurological symptom resolution over time. PANSC symptoms included altered consciousness/confusion, fatigue/malaise, anosmia, dysgeusia and muscle ache/joint pain, on which information was collected at index hospitalization and during follow-up assessments. The analysis considered a time to the resolution of individual and all neurological symptoms. The resulting times were modelled by Weibull regression, assuming mixed-case interval censoring, with sex and age included as covariates. The model results were summarized as cumulative probability functions and age-adjusted and sex-adjusted median times to resolution. We included 6862 hospitalized adults with coronavirus disease 2019, who had follow-up assessments. The median age of the participants was 57 years (39.2% females). Males and females had similar baseline characteristics, except that more males (versus females) were admitted to the intensive care unit (30.5 versus 20.3%) and received mechanical ventilation (17.2 versus 11.8%). Approximately 70% of patients had multiple neurological symptoms at the first follow-up (median = 102 days). Fatigue (49.9%) and myalgia/arthralgia (45.2%) were the most prevalent symptoms of PANSC at the initial follow-up. The reported prevalence in females was generally higher (versus males) for all symptoms. At 12 months, anosmia and dysgeusia were resolved in most patients, although fatigue, altered consciousness and myalgia remained unresolved in >10% of the cohort. Females had a longer time to the resolution (5.2 versus 3.4 months) of neurological symptoms at follow-up for those with more than one neurological symptom. In the multivariable analysis, males were associated with a shorter time to the resolution of symptoms (hazard ratio = 1.53; 95% confidence interval = 1.39-1.69). Intensive care unit admission was associated with a longer time to the resolution of symptoms (hazard ratio = 0.68; 95% confidence interval = 0.60-0.77). Post-discharge stroke was uncommon (0.3% in females and 0.5% in males). Despite the methodological challenges involved in the collection of survey data, this international multi-centre prospective cohort study demonstrated that PANSC following index hospitalization was high. Symptom prevalence was higher and took longer to resolve in females than in males. This supported the fact that while males were sicker during acute illness, females were disproportionately affected by PANSC.
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Affiliation(s)
- Sung-Min Cho
- Neuroscience Critical Care Division, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21278, USA
- Neuroscience Critical Care Division, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21278, USA
- Neuroscience Critical Care Division, Department of Anaesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21278, USA
| | - Lavienraj Premraj
- Australian Centre for Health Services Innovation and Centre for Healthcare Transformation, School of Public Health and Social Work, Queensland University of Technology, Kelvin Grove 4059, Australia
- Griffith University School of Medicine, Gold Coast 4215, Australia
- Critical Care Research Group, The Prince Charles Hospital, Brisbane 4032, Australia
| | - Denise Battaglini
- Department of Surgical Science and Integrated Diagnostic, San Martino Policlinico Hospital, IRCCS for Oncology and Neuroscience, University of Genoa, Genoa 16132, Italy
- Department of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Jonathon Paul Fanning
- Critical Care Research Group, The Prince Charles Hospital, Brisbane 4032, Australia
- Faculty of Medicine, University of Queensland, Brisbane 4006, Australia
| | - Jacky Suen
- Critical Care Research Group, The Prince Charles Hospital, Brisbane 4032, Australia
- Faculty of Medicine, University of Queensland, Brisbane 4006, Australia
| | - Gianluigi Li Bassi
- Australian Centre for Health Services Innovation and Centre for Healthcare Transformation, School of Public Health and Social Work, Queensland University of Technology, Kelvin Grove 4059, Australia
- Critical Care Research Group, The Prince Charles Hospital, Brisbane 4032, Australia
- Faculty of Medicine, University of Queensland, Brisbane 4006, Australia
- Institut d’Investigacions Biomediques August Pi I Sunyer, Barcelona 08036, Spain
| | - John Fraser
- Australian Centre for Health Services Innovation and Centre for Healthcare Transformation, School of Public Health and Social Work, Queensland University of Technology, Kelvin Grove 4059, Australia
- Critical Care Research Group, The Prince Charles Hospital, Brisbane 4032, Australia
- Faculty of Medicine, University of Queensland, Brisbane 4006, Australia
- St Andrew’s War Memorial Hospital, UnitingCare, Spring Hill 4000, Australia
| | - Chiara Robba
- Department of Surgical Science and Integrated Diagnostic, San Martino Policlinico Hospital, IRCCS for Oncology and Neuroscience, University of Genoa, Genoa 16132, Italy
| | - Matthew Griffee
- Department of Anesthesiology, University of Utah, Salt Lake City, UT 84132, USA
| | - Tom Solomon
- Brain Infections Group, Institute of Infection and Global Health, University of Liverpool, Liverpool, L3 5TR, UK
- Department of Neuroscience, University of Liverpool, Liverpool, L3 5TR, UK
- Walton Centre NHS Foundation Trust, Liverpool, L9 7LJ, UK
| | - Malcolm G Semple
- Child Health and Outbreak Medicine, University of Liverpool, Liverpool, L3 5TR, UK
| | - Kenneth Baillie
- Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Louise Sigfrid
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, OX3 7LG, UK
| | - Janet T Scott
- Infectious Disease, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Barbara Wanjiru Citarella
- International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, OX1 2JD, UK
| | - Laura Merson
- Institut d’Investigacions Biomediques August Pi I Sunyer, Barcelona 08036, Spain
| | - Rakesh C Arora
- Department of Surgery, University Hospitals/Case Western Reserve University, Cleveland, OH 44106, USA
| | - Glenn Whitman
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21278, USA
| | - David Thomson
- Department of Anaesthesia and Peri-operative Medicine, University of Cape Town, Cape Town 7700, South Africa
- Division of Critical Care, Groote Schuur Hospital, Cape Town 7925, South Africa
| | - Nicole White
- Australian Centre for Health Services Innovation and Centre for Healthcare Transformation, School of Public Health and Social Work, Queensland University of Technology, Kelvin Grove 4059, Australia
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7
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Nugawela MD, Pinto Pereira SM, Rojas NK, McOwat K, Simmons R, Dalrymple E, Ford T, Garg S, Hargreaves D, Semple MG, Xu L, Shafran R, Stephenson T. Data Resource Profile: the Children and Young People with Long COVID (CLoCk) Study. Int J Epidemiol 2024; 53:dyad158. [PMID: 37990948 PMCID: PMC10859131 DOI: 10.1093/ije/dyad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023] Open
Affiliation(s)
- Manjula D Nugawela
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Snehal M Pinto Pereira
- Research Department of Targeted Intervention, Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London, UK
| | - Natalia K Rojas
- Research Department of Targeted Intervention, Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London, UK
| | - Kelsey McOwat
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, London, UK
| | - Ruth Simmons
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, London, UK
| | - Emma Dalrymple
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Tamsin Ford
- Department of Psychiatry, University of Cambridge, Hershel Smith Building Cambridge Biomedical Campus, Cambridge, UK
| | - Shruti Garg
- Division of Neuroscience, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Child and Adolescent Mental Health Services, Royal Manchester Children’s Hospital, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Dougal Hargreaves
- Mohn Centre for Children’s Health & Wellbeing, School of Public Health, Imperial College London, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
| | - Laila Xu
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Roz Shafran
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Terence Stephenson
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
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8
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Pazukhina E, Rumyantsev M, Baimukhambetova D, Bondarenko E, Markina N, El-Taravi Y, Petrova P, Ezhova A, Andreeva M, Iakovleva E, Bobkova P, Pikuza M, Trefilova A, Abdeeva E, Galiautdinova A, Filippova Y, Bairashevskaia A, Zolotarev A, Bulanov N, DunnGalvin A, Chernyavskaya A, Kondrikova E, Kolotilina A, Gadetskaya S, Ivanova YV, Turina I, Eremeeva A, Fedorova LA, Comberiati P, Peroni DG, Nekliudov N, Genuneit J, Reyes LF, Brackel CLH, Mazankova L, Miroshina A, Samitova E, Borzakova S, Carson G, Sigfrid L, Scott JT, McFarland S, Greenhawt M, Buonsenso D, Semple MG, Warner JO, Olliaro P, Osmanov IM, Korsunskiy AA, Munblit D. Event rates and incidence of post-COVID-19 condition in hospitalised SARS-CoV-2 positive children and young people and controls across different pandemic waves: exposure-stratified prospective cohort study in Moscow (StopCOVID). BMC Med 2024; 22:48. [PMID: 38302974 PMCID: PMC10835884 DOI: 10.1186/s12916-023-03221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/07/2023] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Long-term health outcomes in children and young people (CYP) after COVID-19 infection are not well understood and studies with control groups exposed to other infections are lacking. This study aimed to investigate the incidence of post-COVID-19 condition (PCC) and incomplete recovery in CYP after hospital discharge and compare outcomes between different SARS-CoV-2 variants and non-SARS-CoV-2 infections. METHODS A prospective exposure-stratified cohort study of individuals under 18 years old in Moscow, Russia. Exposed cohorts were paediatric patients admitted with laboratory-confirmed COVID-19 infection between April 2 and December 11, 2020 (Wuhan variant cohort) and between January 12 and February 19, 2022 (Omicron variant cohort). CYP admitted with respiratory and intestinal infections, but negative lateral flow rapid diagnostic test and PCR-test results for SARS-CoV-2, between January 12 and February 19, 2022, served as unexposed reference cohort. Comparison between the 'exposed cohorts' and 'reference cohort' was conducted using 1:1 matching by age and sex. Follow-up data were collected via telephone interviews with parents, utilising the long COVID paediatric protocol and survey developed by the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC). The WHO case definition was used to categorise PCC. RESULTS Of 2595 CYP with confirmed COVID-19, 1707 (65.7%) participated in follow-up interviews, with 1183/1707 (69%) included in the final 'matched' analysis. The median follow-up time post-discharge was 6.7 months. The incidence of PCC was significantly higher in the Wuhan variant cohort (89.7 cases per 1000 person-months, 95% CI 64.3-120.3) compared to post-infection sequalae in the reference cohort (12.2 cases per 1000 person-months, 95% CI 4.9-21.9), whereas the difference with the Omicron variant cohort and reference cohort was not significant. The Wuhan cohort had higher incidence rates of dermatological, fatigue, gastrointestinal, sensory, and sleep manifestations, as well as behavioural and emotional problems than the reference cohort. The only significant difference between Omicron variant cohort and reference cohort was decreased school attendance. When comparing the Wuhan and Omicron variant cohorts, higher incidence of PCC and event rates of fatigue, decreased physical activity, and deterioration of relationships was observed. The rate of incomplete recovery was also significantly higher in the Wuhan variant cohort than in both the reference and the Omicron variant cohorts. CONCLUSIONS Wuhan variant exhibited a propensity for inducing a broad spectrum of physical symptoms and emotional behavioural changes, suggesting a pronounced impact on long-term health outcomes. Conversely, the Omicron variant resulted in fewer post-infection effects no different from common seasonal viral illnesses. This may mean that the Omicron variant and subsequent variants might not lead to the same level of long-term health consequences as earlier variants.
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Affiliation(s)
- Ekaterina Pazukhina
- Laboratory of Health Economics, Institute of Applied Economic Studies, The Russian Presidential Academy of National Economy and Public Administration, Moscow, Russia
- Center for Advanced Financial Planning, Macroeconomic Analysis and Financial Statistics, Financial Research Institute of the Ministry of Finance of the Russian Federation, Moscow, Russia
| | - Mikhail Rumyantsev
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Dina Baimukhambetova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Elena Bondarenko
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Nadezhda Markina
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yasmin El-Taravi
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Polina Petrova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anastasia Ezhova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Margarita Andreeva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ekaterina Iakovleva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Polina Bobkova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Maria Pikuza
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anastasia Trefilova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Elina Abdeeva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Aysylu Galiautdinova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yulia Filippova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anastasiia Bairashevskaia
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Aleksandr Zolotarev
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Nikolay Bulanov
- Tareev Clinic of Internal Diseases, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Audrey DunnGalvin
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- School of Applied Psychology, University College Cork, Cork City, Ireland
| | - Anastasia Chernyavskaya
- Department of Paediatrics and Paediatric Rheumatology, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Elena Kondrikova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anastasia Kolotilina
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Svetlana Gadetskaya
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yulia V Ivanova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Irina Turina
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Alina Eremeeva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ludmila A Fedorova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Pasquale Comberiati
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Diego G Peroni
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Nikita Nekliudov
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Jon Genuneit
- Department of PediatricsPediatric Epidemiology, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Luis Felipe Reyes
- Universidad de La Sabana, School of Medicine, Chía, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Caroline L H Brackel
- Department of Pediatric Pulmonology, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Department of Pediatrics, Tergooi MC, Hilversum, the Netherlands
| | - Lyudmila Mazankova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Elmira Samitova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
- ZA Bashlyaeva Children's Municipal Clinical Hospital, Moscow, Russia
| | - Svetlana Borzakova
- Department of Pediatrics, Russian Medical Academy of Continuing Professional Education of the Ministry of Health, Moscow, Russia
- Research Institute for Healthcare Organization and Medical Management of Moscow Healthcare Department, Moscow, Russia
| | - Gail Carson
- ISARIC Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Louise Sigfrid
- ISARIC Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Janet T Scott
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Matthew Greenhawt
- Department of Pediatrics, Section of Allergy/Immunology, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, USA
| | - Danilo Buonsenso
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Center for Global Health Research and Studies, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - John O Warner
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Piero Olliaro
- ISARIC Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ismail M Osmanov
- Department of Pediatrics, Russian Medical Academy of Continuing Professional Education of the Ministry of Health, Moscow, Russia
- ZA Bashlyaeva Children's Municipal Clinical Hospital, Moscow, Russia
| | - Anatoliy A Korsunskiy
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Daniel Munblit
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.
- Research and Clinical Center for Neuropsychiatry, Moscow, Russia.
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.
- Care for Long Term Conditions Division, Florence Nightingale Faculty of Nursing, Midwifery and Palliative Care, King's College London, London, UK.
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9
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Costigan D, Fenn J, Yen S, Ilott N, Bullers S, Hale J, Greenhalf W, Conibear E, Koycheva A, Madon K, Jahan I, Huang M, Badhan A, Parker E, Rosadas C, Jones K, McClure M, Tedder R, Taylor G, Baillie KJ, Semple MG, Openshaw PJM, Pearson C, Johnson J, Lalvani A, Thornton EE. A pro-inflammatory gut mucosal cytokine response is associated with mild COVID-19 disease and superior induction of serum antibodies. Mucosal Immunol 2024; 17:111-123. [PMID: 37995912 PMCID: PMC10884467 DOI: 10.1016/j.mucimm.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/25/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The relationship between gastrointestinal tract infection, the host immune response, and the clinical outcome of disease is not well understood in COVID-19. We sought to understand the effect of intestinal immune responses to SARS-CoV-2 on patient outcomes including the magnitude of systemic antibody induction. Combining two prospective cohort studies, International Severe Acute Respiratory and emerging Infections Consortium Comprehensive Clinical Characterisations Collaboration (ISARIC4C) and Integrated Network for Surveillance, Trials and Investigations into COVID-19 Transmission (INSTINCT), we acquired samples from 88 COVID-19 cases representing the full spectrum of disease severity and analysed viral RNA and host gut cytokine responses in the context of clinical and virological outcome measures. There was no correlation between the upper respiratory tract and faecal viral loads. Using hierarchical clustering, we identified a group of fecal cytokines including Interleukin-17A, Granulocyte macrophage colony-stimulating factor, Tumor necrosis factorα, Interleukin-23, and S100A8, that were transiently elevated in mild cases and also correlated with the magnitude of systemic anti-Spike-receptor-binding domain antibody induction. Receiver operating characteristic curve analysis showed that expression of these gut cytokines at study enrolment in hospitalised COVID-19 cases was associated negatively with overall clinical severity implicating a protective role in COVID-19. This suggests that a productive intestinal immune response may be beneficial in the response to a respiratory pathogen and a biomarker of a successful barrier response.
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Affiliation(s)
- Dana Costigan
- MRC Translational Immune Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Joe Fenn
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK.
| | - Sandi Yen
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Nicholas Ilott
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Samuel Bullers
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK; Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Jessica Hale
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Emily Conibear
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK
| | | | - Kieran Madon
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK
| | - Ishrat Jahan
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Ming Huang
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Anjna Badhan
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Eleanor Parker
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Carolina Rosadas
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Kelsey Jones
- Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Myra McClure
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Richard Tedder
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Taylor
- Section of Virology, Department of Infectious Disease, Imperial College London, London, UK
| | - Kenneth J Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Peter J M Openshaw
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Claire Pearson
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK; Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Jethro Johnson
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, UK
| | - Ajit Lalvani
- NIHR HPRU in Respiratory Infections, Imperial College London, London, UK
| | - Emily E Thornton
- MRC Translational Immune Discovery Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK; Nuffield Department of Medicine, University of Oxford, UK.
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10
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Mapindra MP, Mahindra MP, McNamara P, Semple MG, Clark H, Madsen J. Respiratory Syncytial Virus Maternal Vaccination in Infants below 6 Months of Age: Meta-Analysis of Safety, Immunogenicity, and Efficacy. Neonatology 2024:1-12. [PMID: 38286126 DOI: 10.1159/000536031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/16/2023] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Severe respiratory syncytial virus (RSV) disease is most prevalent during infancy, particularly in those born prematurely, who benefit least from maternal antibody transfers. Maternal immunization is an attractive prevention leading to vaccine clinical trials. This meta-analysis aimed to evaluate recent maternal RSV vaccine trials. METHODS Following PRISMA-P guidelines for systematic reviews and registered at https://www.crd.york.ac.uk/prospero, this study shortlisted six randomized clinical trials of suitable quality from four databases. Meta-analysis evaluated vaccine safety, immunogenicity, and efficacy in infants and their mothers. RESULTS From random-effects and fixed-effects meta-analysis between trial and control arms, the maternal post-vaccination geometric antibody (Ab) titers showed pooled standard mean differences (SMDs [95% CI]) at delivery of (4.14 [2.91-5.37]), (3.95 [2.79-5.11]), and (12.20 [7.76, 16.64]) for RSV neutralizing Ab A, B, and F IgG, respectively. Vaccine administration was more likely than placebo to cause local pain, erythema, swelling, and systemic myalgia. Furthermore, the Ab levels in infants at birth showed pooled SMDs of each RSV A (3.9 [2.81-4.99]), RSV B (1.86 [1.09-2.62]), and RSV F IgG (2.24 [1.24-3.23]). The overall reduction of RSV-related lower respiratory tract infections and hospitalizations in the first 6 months of life was 52% and 48%, respectively. CONCLUSIONS Not only does antenatal RSV vaccination look safe and immunogenic in vaccinated mothers, but it also reliably provides effective antibody levels in infants and diminishes RSV-related severe disease in infants under 6 months of age.
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Affiliation(s)
| | - Muhammad Pradhiki Mahindra
- Department of Maternal-Fetal Medicine, Institute for Women's Health, University College London, London, UK
| | - Paul McNamara
- Respiratory Medicine, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Malcolm G Semple
- Respiratory Medicine, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Howard Clark
- Department of Neonatology, Institute for Women's Health, University College London, London, UK
| | - Jens Madsen
- Department of Neonatology, Institute for Women's Health, University College London, London, UK
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11
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Deja E, Donohue C, Semple MG, Woolfall K. Stakeholders' perspectives on clinical trial acceptability and approach to consent within a limited timeframe: a mixed methods study. BMJ Open 2024; 14:e077023. [PMID: 38167280 PMCID: PMC10773389 DOI: 10.1136/bmjopen-2023-077023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVES The Bronchiolitis Endotracheal Surfactant Study (BESS) is a randomised controlled trial to determine the efficacy of endo-tracheal surfactant therapy for critically ill infants with bronchiolitis. To explore acceptability of BESS, including approach to consent within a limited time frame, we explored parent and staff experiences of trial involvement in the first two bronchiolitis seasons to inform subsequent trial conduct. DESIGN A mixed-method embedded study involving a site staff survey, questionnaires and interviews with parents approached about BESS. SETTING Fourteen UK paediatric intensive care units. PARTICIPANTS Of the 179 parents of children approached to take part in BESS, 75 parents (of 69 children) took part in the embedded study. Of these, 55/69 (78%) completed a questionnaire, and 15/69 (21%) were interviewed. Thirty-eight staff completed a questionnaire. RESULTS Parents and staff found the trial acceptable. All constructs of the Adapted Theoretical Framework of Acceptability were met. Parents viewed surfactant as being low risk and hoped their child's participation would help others in the future. Although parents supported research without prior consent in studies of time critical interventions, they believed there was sufficient time to consider this trial. Parents recommended that prospective informed consent should continue to be sought for BESS. Many felt that the time between the consent process and intervention being administered took too long and should be 'streamlined' to avoid delays in administration of trial interventions. Staff described how the training and trial processes worked well, yet patients were missed due to lack of staff to deliver the intervention, particularly at weekends. CONCLUSION Parents and staff supported BESS trial and highlighted aspects of the protocol, which should be refined, including a streamlined informed consent process. Findings will be useful to inform proportionate approaches to consent in future paediatric trials where there is a short timeframe for consent discussions. TRIAL REGISTRATION NUMBER ISRCTN11746266.
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Affiliation(s)
- Elizabeth Deja
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
| | - Chloe Donohue
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Kerry Woolfall
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
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12
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Burnside G, Cheyne CP, Leeming G, Humann M, Darby A, Green MA, Crozier A, Maskell S, O’Halloran K, Musi E, Carmi E, Khan N, Fisher D, Corcoran R, Dunning J, Edmunds WJ, Tharmaratnam K, Hughes DM, Malki-Epshtein L, Cook M, Roberts BM, Gallagher E, Howell K, Chand M, Kemp R, Boulter M, Fowler T, Semple MG, Coffey E, Ashton M, García-Fiñana M, Buchan IE. COVID-19 risk mitigation in reopening mass cultural events: population-based observational study for the UK Events Research Programme in Liverpool City Region. J R Soc Med 2024; 117:11-23. [PMID: 37351911 PMCID: PMC10858718 DOI: 10.1177/01410768231182389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/25/2023] [Indexed: 06/24/2023] Open
Abstract
OBJECTIVES To understand severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission risks, perceived risks and the feasibility of risk mitigations from experimental mass cultural events before coronavirus disease 2019 (COVID-19) restrictions were lifted. DESIGN Prospective, population-wide observational study. SETTING Four events (two nightclubs, an outdoor music festival and a business conference) open to Liverpool City Region UK residents, requiring a negative lateral flow test (LFT) within the 36 h before the event, but not requiring social distancing or face-coverings. PARTICIPANTS A total of 12,256 individuals attending one or more events between 28 April and 2 May 2021. MAIN OUTCOME MEASURES SARS-CoV-2 infections detected using audience self-swabbed (5-7 days post-event) polymerase chain reaction (PCR) tests, with viral genomic analysis of cases, plus linked National Health Service COVID-19 testing data. Audience experiences were gathered via questionnaires, focus groups and social media. Indoor CO2 concentrations were monitored. RESULTS A total of 12 PCR-positive cases (likely 4 index, 8 primary or secondary), 10 from the nightclubs. Two further cases had positive LFTs but no PCR. A total of 11,896 (97.1%) participants with scanned tickets were matched to a negative pre-event LFT: 4972 (40.6%) returned a PCR within a week. CO2 concentrations showed areas for improving ventilation at the nightclubs. Population infection rates were low, yet with a concurrent outbreak of >50 linked cases around a local swimming pool without equivalent risk mitigations. Audience anxiety was low and enjoyment high. CONCLUSIONS We observed minor SARS-CoV-2 transmission and low perceived risks around events when prevalence was low and risk mitigations prominent. Partnership between audiences, event organisers and public health services, supported by information systems with real-time linked data, can improve health security for mass cultural events.
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Affiliation(s)
- Girvan Burnside
- Deparment of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GL, UK
| | - Christopher P Cheyne
- Deparment of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GL, UK
| | - Gary Leeming
- Deparment of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GL, UK
| | - Michael Humann
- Department of Psychology, University of Liverpool, Liverpool L69 7ZA, UK
| | - Alistair Darby
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Mark A Green
- Department of Geography and Planning, University of Liverpool L69 3BX, Liverpool, UK
| | - Alexander Crozier
- Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Simon Maskell
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3BX, UK
| | - Kay O’Halloran
- Department of Communication and Media, University of Liverpool, Liverpool L69 7ZG, UK
| | - Elena Musi
- Department of Communication and Media, University of Liverpool, Liverpool L69 7ZG, UK
| | - Elinor Carmi
- Department of Sociology and Criminology, City University, London EC1V 0HB, UK
| | - Naila Khan
- Department of Primary Care & Mental Health, Institute of Population Health, University of Liverpool, Liverpool L69 3BX, UK
| | - Debra Fisher
- Department of Primary Care & Mental Health, Institute of Population Health, University of Liverpool, Liverpool L69 3BX, UK
| | - Rhiannon Corcoran
- Department of Primary Care & Mental Health, Institute of Population Health, University of Liverpool, Liverpool L69 3BX, UK
| | - Jake Dunning
- Pandemic Sciences Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - W John Edmunds
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Kukatharmini Tharmaratnam
- Deparment of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GL, UK
| | - David M Hughes
- Deparment of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GL, UK
| | - Liora Malki-Epshtein
- Department of Civil, Environmental and Geomatic Engineering, University College London, London WC1E 6BT, UK
| | - Malcolm Cook
- Building Energy Research Group, School of Architecture, Building and Civil Engineering, Loughborough University, Loughborough LE11 3TU, UK
| | - Ben M Roberts
- Building Energy Research Group, School of Architecture, Building and Civil Engineering, Loughborough University, Loughborough LE11 3TU, UK
| | - Eileen Gallagher
- Clinical and Public Health Group, UK Health Security Agency, London SW1P 3JR, UK
| | - Kate Howell
- Clinical and Public Health Group, UK Health Security Agency, London SW1P 3JR, UK
| | - Meera Chand
- Clinical and Public Health Group, UK Health Security Agency, London SW1P 3JR, UK
| | - Robin Kemp
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Matthew Boulter
- Clinical and Public Health Group, UK Health Security Agency, London SW1P 3JR, UK
| | - Tom Fowler
- Clinical and Public Health Group, UK Health Security Agency, London SW1P 3JR, UK
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Malcolm G Semple
- Department of Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Emer Coffey
- Liverpool City Council, Liverpool L3 1AH, UK
| | - Matt Ashton
- Liverpool City Council, Liverpool L3 1AH, UK
- Department of Public Health, Policy and Systems, Institute of Population Health, University of Liverpool, Liverpool L69 3GB, UK
| | - The COVID-19 Genomics UK (COG-UK) Consortium
- Deparment of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GL, UK
- Department of Psychology, University of Liverpool, Liverpool L69 7ZA, UK
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Department of Geography and Planning, University of Liverpool L69 3BX, Liverpool, UK
- Division of Biosciences, University College London, London WC1E 6BT, UK
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3BX, UK
- Department of Communication and Media, University of Liverpool, Liverpool L69 7ZG, UK
- Department of Sociology and Criminology, City University, London EC1V 0HB, UK
- Department of Primary Care & Mental Health, Institute of Population Health, University of Liverpool, Liverpool L69 3BX, UK
- Pandemic Sciences Institute, University of Oxford, Oxford OX3 7DQ, UK
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
- Department of Civil, Environmental and Geomatic Engineering, University College London, London WC1E 6BT, UK
- Building Energy Research Group, School of Architecture, Building and Civil Engineering, Loughborough University, Loughborough LE11 3TU, UK
- Clinical and Public Health Group, UK Health Security Agency, London SW1P 3JR, UK
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
- Liverpool City Council, Liverpool L3 1AH, UK
- Department of Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Department of Public Health, Policy and Systems, Institute of Population Health, University of Liverpool, Liverpool L69 3GB, UK
- *Shared senior authorship
| | - Marta García-Fiñana
- Deparment of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GL, UK
| | - Iain E Buchan
- Department of Public Health, Policy and Systems, Institute of Population Health, University of Liverpool, Liverpool L69 3GB, UK
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13
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Michael BD, Dunai C, Needham EJ, Tharmaratnam K, Williams R, Huang Y, Boardman SA, Clark JJ, Sharma P, Subramaniam K, Wood GK, Collie C, Digby R, Ren A, Norton E, Leibowitz M, Ebrahimi S, Fower A, Fox H, Tato E, Ellul MA, Sunderland G, Held M, Hetherington C, Egbe FN, Palmos A, Stirrups K, Grundmann A, Chiollaz AC, Sanchez JC, Stewart JP, Griffiths M, Solomon T, Breen G, Coles AJ, Kingston N, Bradley JR, Chinnery PF, Cavanagh J, Irani SR, Vincent A, Baillie JK, Openshaw PJ, Semple MG, Taams LS, Menon DK. Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses. Nat Commun 2023; 14:8487. [PMID: 38135686 PMCID: PMC10746705 DOI: 10.1038/s41467-023-42320-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/06/2023] [Indexed: 12/24/2023] Open
Abstract
To understand neurological complications of COVID-19 better both acutely and for recovery, we measured markers of brain injury, inflammatory mediators, and autoantibodies in 203 hospitalised participants; 111 with acute sera (1-11 days post-admission) and 92 convalescent sera (56 with COVID-19-associated neurological diagnoses). Here we show that compared to 60 uninfected controls, tTau, GFAP, NfL, and UCH-L1 are increased with COVID-19 infection at acute timepoints and NfL and GFAP are significantly higher in participants with neurological complications. Inflammatory mediators (IL-6, IL-12p40, HGF, M-CSF, CCL2, and IL-1RA) are associated with both altered consciousness and markers of brain injury. Autoantibodies are more common in COVID-19 than controls and some (including against MYL7, UCH-L1, and GRIN3B) are more frequent with altered consciousness. Additionally, convalescent participants with neurological complications show elevated GFAP and NfL, unrelated to attenuated systemic inflammatory mediators and to autoantibody responses. Overall, neurological complications of COVID-19 are associated with evidence of neuroglial injury in both acute and late disease and these correlate with dysregulated innate and adaptive immune responses acutely.
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Affiliation(s)
- Benedict D Michael
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK.
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK.
- The Walton Centre NHS Foundation Trust, Liverpool, L9 7BB, UK.
| | - Cordelia Dunai
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK
| | - Edward J Needham
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kukatharmini Tharmaratnam
- Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, L69 3GF, UK
| | - Robyn Williams
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Departments of Neurology and Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yun Huang
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Sarah A Boardman
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Jordan J Clark
- University of Liverpool, Liverpool, L69 7BE, UK
- Department of Microbiology, Icahn School of Medicine, Mount Sinai, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine, Mount Sinai, NY, 10029, USA
| | - Parul Sharma
- Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Krishanthi Subramaniam
- Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Greta K Wood
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Ceryce Collie
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Richard Digby
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Alexander Ren
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Emma Norton
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Maya Leibowitz
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Soraya Ebrahimi
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Andrew Fower
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah Fox
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Esteban Tato
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
- NIHR Maudsley Biomedical Research Centre, King's College London, London, SE5 8AF, UK
| | - Mark A Ellul
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- The Walton Centre NHS Foundation Trust, Liverpool, L9 7BB, UK
| | - Geraint Sunderland
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Marie Held
- Centre for Cell Imaging, Liverpool Shared Research Facilities, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Claire Hetherington
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Franklyn N Egbe
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Alish Palmos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
- NIHR Maudsley Biomedical Research Centre, King's College London, London, SE5 8AF, UK
| | - Kathy Stirrups
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Alexander Grundmann
- Clinical Neurosciences, Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, SO17 1BF, UK
- Department of Neurology, Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Anne-Cecile Chiollaz
- Département de médecine interne des spécialités (DEMED), University of Geneva, Geneva, CH-1211, Switzerland
| | - Jean-Charles Sanchez
- Département de médecine interne des spécialités (DEMED), University of Geneva, Geneva, CH-1211, Switzerland
| | - James P Stewart
- Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Michael Griffiths
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Tom Solomon
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK
- The Walton Centre NHS Foundation Trust, Liverpool, L9 7BB, UK
- The Pandemic Institute, Liverpool, L7 3FA, UK
| | - Gerome Breen
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
- NIHR Maudsley Biomedical Research Centre, King's College London, London, SE5 8AF, UK
| | - Alasdair J Coles
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge, CB2 0QQ, UK
| | - John R Bradley
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, CB2 0QQ, UK
| | - Jonathan Cavanagh
- Centre for Immunology, School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Departments of Neurology and Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Angela Vincent
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Peter J Openshaw
- National Heart and Lung Institute, Imperial College London, London, SW7 2BX, UK
- Imperial College Healthcare NHS Trust, London, W2 1NY, UK
| | - Malcolm G Semple
- Clinical Infection, Microbiology, and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, L69 7BE, UK
- Respiratory Unit, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, L14 5AB, UK
| | - Leonie S Taams
- Centre for Inflammation Biology and Cancer Immunology, King's College London, London, SE1 9RT, UK
| | - David K Menon
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
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14
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Sidhu JK, Siggins MK, Liew F, Russell CD, Uruchurtu ASS, Davis C, Turtle L, Moore SC, Hardwick HE, Oosthuyzen W, Thomson EC, Semple MG, Baillie JK, Openshaw PJM, Thwaites RS. Delayed mucosal anti-viral responses despite robust peripheral inflammation in fatal COVID-19. J Infect Dis 2023:jiad590. [PMID: 38134401 DOI: 10.1093/infdis/jiad590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND While inflammatory and immune responses to SARS-CoV-2 infection in peripheral blood are extensively described, responses at the upper respiratory mucosal site of initial infection are relatively poorly defined. We sought to identify mucosal cytokine/chemokine signatures that distinguished COVID-19 severity categories, and relate these to disease progression and peripheral inflammation. METHODS We measured 35 cytokines and chemokines in nasal samples from 274 patients hospitalised with COVID-19. Analysis considered the timing of sampling during disease, as either the early (0-5 days post-symptom onset) or late (6-20 days post-symptom onset). RESULTS Patients that survived severe COVID-19 showed IFN-dominated mucosal immune responses (IFN-γ, CXCL10 and CXCL13) early in infection. These early mucosal responses were absent in patients that would progress to fatal disease despite equivalent SARS-CoV-2 viral load. Mucosal inflammation in later disease was dominated by IL-2, IL-10, IFN-γ, and IL-12p70, which scaled with severity but did not differentiate patients who would survive or succumb to disease. Cytokines and chemokines in the mucosa showed distinctions from responses evident in the peripheral blood, particularly during fatal disease. CONCLUSIONS Defective early mucosal anti-viral responses anticipate fatal COVID-19 but are not associated with viral load. Early mucosal immune responses may define the trajectory of severe COVID-19.
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Affiliation(s)
- Jasmin K Sidhu
- National Heart and Lung Institute, Imperial College London, U.K
| | | | - Felicity Liew
- National Heart and Lung Institute, Imperial College London, U.K
| | - Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Edinburgh, U.K
| | | | | | - Lance Turtle
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
- Tropical and Infectious Disease unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), U.K
| | - Shona C Moore
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
| | - Hayley E Hardwick
- Dept of Clinical Infection, Microbiology and Immunology, University of Liverpool, U.K
| | | | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, U.K
- London School of Hygiene and Tropical Medicine, London, U.K
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, U.K
- Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, U.K
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, U.K
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, U.K
| | | | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, U.K
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15
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McOwat K, Pinto Pereira SM, Nugawela MD, Ladhani SN, Newlands F, Stephenson T, Simmons R, Semple MG, Segal T, Buszewicz M, Heyman I, Chalder T, Ford T, Dalrymple E, Shafran R. The CLoCk study: A retrospective exploration of loneliness in children and young people during the COVID-19 pandemic, in England. PLoS One 2023; 18:e0294165. [PMID: 37988366 PMCID: PMC10662715 DOI: 10.1371/journal.pone.0294165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND During the COVID-19 pandemic children and young people (CYP) were socially restricted during a stage of life crucial to development, potentially putting an already vulnerable population at higher risk of loneliness, social isolation, and poorer wellbeing. The objectives of this study are to conduct an exploratory analysis into loneliness before and during the pandemic, and determine which self-reported factors are associated with loneliness. METHODS AND FINDINGS Participants from The Children with Long COVID (CLoCk) national study were invited to take part via an online survey, with a total of 31,017 participants taking part, 31,016 of which reported on their experience of loneliness. Participants retrospectively answered questions on demographics, lifestyle, physical health and mental health and loneliness before the pandemic and at the time of answering the survey. Before the pandemic 6.5% (2,006/31,016) of participants reported experiencing loneliness "Often/Always" and at the time of survey completion 17.4% (5,395/31,016) reported feeling lonelier. There was an association between meeting the research definition of long COVID and loneliness [3.49 OR, 95%CI 3.28-3.72]. CYP who reported feeling lonelier at the time of the survey than before the pandemic were assigned female at birth, older CYP, those from Black/African/Caribbean/Black British or other ethnicity groups, those that had 3-4 siblings and lived in more deprived areas. CONCLUSIONS We demonstrate associations between multiple factors and experiences of loneliness during the pandemic. There is a need for a multi-faceted integrated approach when developing interventions targeted at loneliness. It is important to follow up the CYP involved at regular intervals to investigate the progression of their experience of loneliness over time.
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Affiliation(s)
- Kelsey McOwat
- Immunisations and Vaccine Preventable Diseases Department, UK Health Security Agency, London, United Kingdom
| | - Snehal M. Pinto Pereira
- Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Manjula D. Nugawela
- University College London—Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Shamez N. Ladhani
- Immunisations and Vaccine Preventable Diseases Department, UK Health Security Agency, London, United Kingdom
| | - Fiona Newlands
- University College London—Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Terence Stephenson
- University College London—Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ruth Simmons
- Immunisations and Vaccine Preventable Diseases Department, UK Health Security Agency, London, United Kingdom
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, United Kingdom
- Respiratory Medicine, Alder Hey Children’s Hospital, Institute in The Park, University of Liverpool, Liverpool, United Kingdom
| | - Terry Segal
- Department of Paediatrics and Adolescence, University College London Hospital, London, United Kingdom
| | - Marta Buszewicz
- University College London—Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Isobel Heyman
- University College London—Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Trudie Chalder
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Tamsin Ford
- Department of Psychiatry, University of Cambridge, Hershel Smith Building Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Emma Dalrymple
- University College London—Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Roz Shafran
- University College London—Great Ormond Street Institute of Child Health, London, United Kingdom
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16
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Swets MC, Kerr S, Scott-Brown J, Brown AB, Gupta R, Millar JE, Spata E, McCurrach F, Bretherick AD, Docherty A, Harrison D, Rowan K, Young N, Groeneveld GH, Dunning J, Nguyen-Van-Tam JS, Openshaw P, Horby PW, Harrison E, Staplin N, Semple MG, Lone N, Baillie JK. Evaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity. Nat Commun 2023; 14:7374. [PMID: 37968269 PMCID: PMC10651917 DOI: 10.1038/s41467-023-42205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023] Open
Abstract
Choosing optimal outcome measures maximizes statistical power, accelerates discovery and improves reliability in early-phase trials. We devised and evaluated a modification to a pragmatic measure of oxygenation function, the [Formula: see text] ratio. Because of the ceiling effect in oxyhaemoglobin saturation, [Formula: see text] ratio ceases to reflect pulmonary oxygenation function at high [Formula: see text] values. We found that the correlation of [Formula: see text] with the reference standard ([Formula: see text]/[Formula: see text] ratio) improves substantially when excluding [Formula: see text] and refer to this measure as [Formula: see text]. Using observational data from 39,765 hospitalised COVID-19 patients, we demonstrate that [Formula: see text] is predictive of mortality, and compare the sample sizes required for trials using four different outcome measures. We show that a significant difference in outcome could be detected with the smallest sample size using [Formula: see text]. We demonstrate that [Formula: see text] is an effective intermediate outcome measure in COVID-19. It is a non-invasive measurement, representative of disease severity and provides greater statistical power.
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Affiliation(s)
- Maaike C Swets
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Department of Infectious Diseases, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Steven Kerr
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - Adam B Brown
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rishi Gupta
- Institute for Global Health, University College London, London, UK
| | | | - Enti Spata
- Medical Research Council Population Health Research Unit at the University of Oxford, Nuffield Department of Population Health (NDPH), Oxford, UK
| | - Fiona McCurrach
- EMERGE, NHS Lothian, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Annemarie Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - David Harrison
- Intensive Care National Audit & Research Centre, London, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | - Neil Young
- Department of Anaesthesia, Critical Care and Pain Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Geert H Groeneveld
- Department of Infectious Diseases, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Jake Dunning
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | | | - Peter Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Peter W Horby
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Ewen Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Natalie Staplin
- Medical Research Council Population Health Research Unit at the University of Oxford, Nuffield Department of Population Health (NDPH), Oxford, UK
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Nazir Lone
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, UK.
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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17
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Raman B, McCracken C, Cassar MP, Moss AJ, Finnigan L, Samat AHA, Ogbole G, Tunnicliffe EM, Alfaro-Almagro F, Menke R, Xie C, Gleeson F, Lukaschuk E, Lamlum H, McGlynn K, Popescu IA, Sanders ZB, Saunders LC, Piechnik SK, Ferreira VM, Nikolaidou C, Rahman NM, Ho LP, Harris VC, Shikotra A, Singapuri A, Pfeffer P, Manisty C, Kon OM, Beggs M, O'Regan DP, Fuld J, Weir-McCall JR, Parekh D, Steeds R, Poinasamy K, Cuthbertson DJ, Kemp GJ, Semple MG, Horsley A, Miller CA, O'Brien C, Shah AM, Chiribiri A, Leavy OC, Richardson M, Elneima O, McAuley HJC, Sereno M, Saunders RM, Houchen-Wolloff L, Greening NJ, Bolton CE, Brown JS, Choudhury G, Diar Bakerly N, Easom N, Echevarria C, Marks M, Hurst JR, Jones MG, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Howard LS, Jacob J, Man WDC, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Singh SJ, Thomas DC, Toshner M, Lewis KE, Heaney LG, Harrison EM, Kerr S, Docherty AB, Lone NI, Quint J, Sheikh A, Zheng B, Jenkins RG, Cox E, Francis S, Halling-Brown M, Chalmers JD, Greenwood JP, Plein S, Hughes PJC, Thompson AAR, Rowland-Jones SL, Wild JM, Kelly M, Treibel TA, Bandula S, Aul R, Miller K, Jezzard P, Smith S, Nichols TE, McCann GP, Evans RA, Wain LV, Brightling CE, Neubauer S, Baillie JK, Shaw A, Hairsine B, Kurasz C, Henson H, Armstrong L, Shenton L, Dobson H, Dell A, Lucey A, Price A, Storrie A, Pennington C, Price C, Mallison G, Willis G, Nassa H, Haworth J, Hoare M, Hawkings N, Fairbairn S, Young S, Walker S, Jarrold I, Sanderson A, David C, Chong-James K, Zongo O, James WY, Martineau A, King B, Armour C, McAulay D, Major E, McGinness J, McGarvey L, Magee N, Stone R, Drain S, Craig T, Bolger A, Haggar A, Lloyd A, Subbe C, Menzies D, Southern D, McIvor E, Roberts K, Manley R, Whitehead V, Saxon W, Bularga A, Mills NL, El-Taweel H, Dawson J, Robinson L, Saralaya D, Regan K, Storton K, Brear L, Amoils S, Bermperi A, Elmer A, Ribeiro C, Cruz I, Taylor J, Worsley J, Dempsey K, Watson L, Jose S, Marciniak S, Parkes M, McQueen A, Oliver C, Williams J, Paradowski K, Broad L, Knibbs L, Haynes M, Sabit R, Milligan L, Sampson C, Hancock A, Evenden C, Lynch C, Hancock K, Roche L, Rees M, Stroud N, Thomas-Woods T, Heller S, Robertson E, Young B, Wassall H, Babores M, Holland M, Keenan N, Shashaa S, Price C, Beranova E, Ramos H, Weston H, Deery J, Austin L, Solly R, Turney S, Cosier T, Hazelton T, Ralser M, Wilson A, Pearce L, Pugmire S, Stoker W, McCormick W, Dewar A, Arbane G, Kaltsakas G, Kerslake H, Rossdale J, Bisnauthsing K, Aguilar Jimenez LA, Martinez LM, Ostermann M, Magtoto MM, Hart N, Marino P, Betts S, Solano TS, Arias AM, Prabhu A, Reed A, Wrey Brown C, Griffin D, Bevan E, Martin J, Owen J, Alvarez Corral M, Williams N, Payne S, Storrar W, Layton A, Lawson C, Mills C, Featherstone J, Stephenson L, Burdett T, Ellis Y, Richards A, Wright C, Sykes DL, Brindle K, Drury K, Holdsworth L, Crooks MG, Atkin P, Flockton R, Thackray-Nocera S, Mohamed A, Taylor A, Perkins E, Ross G, McGuinness H, Tench H, Phipps J, Loosley R, Wolf-Roberts R, Coetzee S, Omar Z, Ross A, Card B, Carr C, King C, Wood C, Copeland D, Calvelo E, Chilvers ER, Russell E, Gordon H, Nunag JL, Schronce J, March K, Samuel K, Burden L, Evison L, McLeavey L, Orriss-Dib L, Tarusan L, Mariveles M, Roy M, Mohamed N, Simpson N, Yasmin N, Cullinan P, Daly P, Haq S, Moriera S, Fayzan T, Munawar U, Nwanguma U, Lingford-Hughes A, Altmann D, Johnston D, Mitchell J, Valabhji J, Price L, Molyneaux PL, Thwaites RS, Walsh S, Frankel A, Lightstone L, Wilkins M, Willicombe M, McAdoo S, Touyz R, Guerdette AM, Warwick K, Hewitt M, Reddy R, White S, McMahon A, Hoare A, Knighton A, Ramos A, Te A, Jolley CJ, Speranza F, Assefa-Kebede H, Peralta I, Breeze J, Shevket K, Powell N, Adeyemi O, Dulawan P, Adrego R, Byrne S, Patale S, Hayday A, Malim M, Pariante C, Sharpe C, Whitney J, Bramham K, Ismail K, Wessely S, Nicholson T, Ashworth A, Humphries A, Tan AL, Whittam B, Coupland C, Favager C, Peckham D, Wade E, Saalmink G, Clarke J, Glossop J, Murira J, Rangeley J, Woods J, Hall L, Dalton M, Window N, Beirne P, Hardy T, Coakley G, Turtle L, Berridge A, Cross A, Key AL, Rowe A, Allt AM, Mears C, Malein F, Madzamba G, Hardwick HE, Earley J, Hawkes J, Pratt J, Wyles J, Tripp KA, Hainey K, Allerton L, Lavelle-Langham L, Melling L, Wajero LO, Poll L, Noonan MJ, French N, Lewis-Burke N, Williams-Howard SA, Cooper S, Kaprowska S, Dobson SL, Marsh S, Highett V, Shaw V, Beadsworth M, Defres S, Watson E, Tiongson GF, Papineni P, Gurram S, Diwanji SN, Quaid S, Briggs A, Hastie C, Rogers N, Stensel D, Bishop L, McIvor K, Rivera-Ortega P, Al-Sheklly B, Avram C, Faluyi D, Blaikely J, Piper Hanley K, Radhakrishnan K, Buch M, Hanley NA, Odell N, Osbourne R, Stockdale S, Felton T, Gorsuch T, Hussell T, Kausar Z, Kabir T, McAllister-Williams H, Paddick S, Burn D, Ayoub A, Greenhalgh A, Sayer A, Young A, Price D, Burns G, MacGowan G, Fisher H, Tedd H, Simpson J, Jiwa K, Witham M, Hogarth P, West S, Wright S, McMahon MJ, Neill P, Dougherty A, Morrow A, Anderson D, Grieve D, Bayes H, Fallon K, Mangion K, Gilmour L, Basu N, Sykes R, Berry C, McInnes IB, Donaldson A, Sage EK, Barrett F, Welsh B, Bell M, Quigley J, Leitch K, Macliver L, Patel M, Hamil R, Deans A, Furniss J, Clohisey S, Elliott A, Solstice AR, Deas C, Tee C, Connell D, Sutherland D, George J, Mohammed S, Bunker J, Holmes K, Dipper A, Morley A, Arnold D, Adamali H, Welch H, Morrison L, Stadon L, Maskell N, Barratt S, Dunn S, Waterson S, Jayaraman B, Light T, Selby N, Hosseini A, Shaw K, Almeida P, Needham R, Thomas AK, Matthews L, Gupta A, Nikolaidis A, Dupont C, Bonnington J, Chrystal M, Greenhaff PL, Linford S, Prosper S, Jang W, Alamoudi A, Bloss A, Megson C, Nicoll D, Fraser E, Pacpaco E, Conneh F, Ogg G, McShane H, Koychev I, Chen J, Pimm J, Ainsworth M, Pavlides M, Sharpe M, Havinden-Williams M, Petousi N, Talbot N, Carter P, Kurupati P, Dong T, Peng Y, Burns A, Kanellakis N, Korszun A, Connolly B, Busby J, Peto T, Patel B, Nolan CM, Cristiano D, Walsh JA, Liyanage K, Gummadi M, Dormand N, Polgar O, George P, Barker RE, Patel S, Price L, Gibbons M, Matila D, Jarvis H, Lim L, Olaosebikan O, Ahmad S, Brill S, Mandal S, Laing C, Michael A, Reddy A, Johnson C, Baxendale H, Parfrey H, Mackie J, Newman J, Pack J, Parmar J, Paques K, Garner L, Harvey A, Summersgill C, Holgate D, Hardy E, Oxton J, Pendlebury J, McMorrow L, Mairs N, Majeed N, Dark P, Ugwuoke R, Knight S, Whittaker S, Strong-Sheldrake S, Matimba-Mupaya W, Chowienczyk P, Pattenadk D, Hurditch E, Chan F, Carborn H, Foot H, Bagshaw J, Hockridge J, Sidebottom J, Lee JH, Birchall K, Turner K, Haslam L, Holt L, Milner L, Begum M, Marshall M, Steele N, Tinker N, Ravencroft P, Butcher R, Misra S, Walker S, Coburn Z, Fairman A, Ford A, Holbourn A, Howell A, Lawrie A, Lye A, Mbuyisa A, Zawia A, Holroyd-Hind B, Thamu B, Clark C, Jarman C, Norman C, Roddis C, Foote D, Lee E, Ilyas F, Stephens G, Newell H, Turton H, Macharia I, Wilson I, Cole J, McNeill J, Meiring J, Rodger J, Watson J, Chapman K, Harrington K, Chetham L, Hesselden L, Nwafor L, Dixon M, Plowright M, Wade P, Gregory R, Lenagh R, Stimpson R, Megson S, Newman T, Cheng Y, Goodwin C, Heeley C, Sissons D, Sowter D, Gregory H, Wynter I, Hutchinson J, Kirk J, Bennett K, Slack K, Allsop L, Holloway L, Flynn M, Gill M, Greatorex M, Holmes M, Buckley P, Shelton S, Turner S, Sewell TA, Whitworth V, Lovegrove W, Tomlinson J, Warburton L, Painter S, Vickers C, Redwood D, Tilley J, Palmer S, Wainwright T, Breen G, Hotopf M, Dunleavy A, Teixeira J, Ali M, Mencias M, Msimanga N, Siddique S, Samakomva T, Tavoukjian V, Forton D, Ahmed R, Cook A, Thaivalappil F, Connor L, Rees T, McNarry M, Williams N, McCormick J, McIntosh J, Vere J, Coulding M, Kilroy S, Turner V, Butt AT, Savill H, Fraile E, Ugoji J, Landers G, Lota H, Portukhay S, Nasseri M, Daniels A, Hormis A, Ingham J, Zeidan L, Osborne L, Chablani M, Banerjee A, David A, Pakzad A, Rangelov B, Williams B, Denneny E, Willoughby J, Xu M, Mehta P, Batterham R, Bell R, Aslani S, Lilaonitkul W, Checkley A, Bang D, Basire D, Lomas D, Wall E, Plant H, Roy K, Heightman M, Lipman M, Merida Morillas M, Ahwireng N, Chambers RC, Jastrub R, Logan S, Hillman T, Botkai A, Casey A, Neal A, Newton-Cox A, Cooper B, Atkin C, McGee C, Welch C, Wilson D, Sapey E, Qureshi H, Hazeldine J, Lord JM, Nyaboko J, Short J, Stockley J, Dasgin J, Draxlbauer K, Isaacs K, Mcgee K, Yip KP, Ratcliffe L, Bates M, Ventura M, Ahmad Haider N, Gautam N, Baggott R, Holden S, Madathil S, Walder S, Yasmin S, Hiwot T, Jackson T, Soulsby T, Kamwa V, Peterkin Z, Suleiman Z, Chaudhuri N, Wheeler H, Djukanovic R, Samuel R, Sass T, Wallis T, Marshall B, Childs C, Marouzet E, Harvey M, Fletcher S, Dickens C, Beckett P, Nanda U, Daynes E, Charalambou A, Yousuf AJ, Lea A, Prickett A, Gooptu B, Hargadon B, Bourne C, Christie C, Edwardson C, Lee D, Baldry E, Stringer E, Woodhead F, Mills G, Arnold H, Aung H, Qureshi IN, Finch J, Skeemer J, Hadley K, Khunti K, Carr L, Ingram L, Aljaroof M, Bakali M, Bakau M, Baldwin M, Bourne M, Pareek M, Soares M, Tobin M, Armstrong N, Brunskill N, Goodman N, Cairns P, Haldar P, McCourt P, Dowling R, Russell R, Diver S, Edwards S, Glover S, Parker S, Siddiqui S, Ward TJC, Mcnally T, Thornton T, Yates T, Ibrahim W, Monteiro W, Thickett D, Wilkinson D, Broome M, McArdle P, Upthegrove R, Wraith D, Langenberg C, Summers C, Bullmore E, Heeney JL, Schwaeble W, Sudlow CL, Adeloye D, Newby DE, Rudan I, Shankar-Hari M, Thorpe M, Pius R, Walmsley S, McGovern A, Ballard C, Allan L, Dennis J, Cavanagh J, Petrie J, O'Donnell K, Spears M, Sattar N, MacDonald S, Guthrie E, Henderson M, Guillen Guio B, Zhao B, Lawson C, Overton C, Taylor C, Tong C, Mukaetova-Ladinska E, Turner E, Pearl JE, Sargant J, Wormleighton J, Bingham M, Sharma M, Steiner M, Samani N, Novotny P, Free R, Allen RJ, Finney S, Terry S, Brugha T, Plekhanova T, McArdle A, Vinson B, Spencer LG, Reynolds W, Ashworth M, Deakin B, Chinoy H, Abel K, Harvie M, Stanel S, Rostron A, Coleman C, Baguley D, Hufton E, Khan F, Hall I, Stewart I, Fabbri L, Wright L, Kitterick P, Morriss R, Johnson S, Bates A, Antoniades C, Clark D, Bhui K, Channon KM, Motohashi K, Sigfrid L, Husain M, Webster M, Fu X, Li X, Kingham L, Klenerman P, Miiler K, Carson G, Simons G, Huneke N, Calder PC, Baldwin D, Bain S, Lasserson D, Daines L, Bright E, Stern M, Crisp P, Dharmagunawardena R, Reddington A, Wight A, Bailey L, Ashish A, Robinson E, Cooper J, Broadley A, Turnbull A, Brookes C, Sarginson C, Ionita D, Redfearn H, Elliott K, Barman L, Griffiths L, Guy Z, Gill R, Nathu R, Harris E, Moss P, Finnigan J, Saunders K, Saunders P, Kon S, Kon SS, O'Brien L, Shah K, Shah P, Richardson E, Brown V, Brown M, Brown J, Brown J, Brown A, Brown A, Brown M, Choudhury N, Jones S, Jones H, Jones L, Jones I, Jones G, Jones H, Jones D, Davies F, Davies E, Davies K, Davies G, Davies GA, Howard K, Porter J, Rowland J, Rowland A, Scott K, Singh S, Singh C, Thomas S, Thomas C, Lewis V, Lewis J, Lewis D, Harrison P, Francis C, Francis R, Hughes RA, Hughes J, Hughes AD, Thompson T, Kelly S, Smith D, Smith N, Smith A, Smith J, Smith L, Smith S, Evans T, Evans RI, Evans D, Evans R, Evans H, Evans J. Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study. Lancet Respir Med 2023; 11:1003-1019. [PMID: 37748493 PMCID: PMC7615263 DOI: 10.1016/s2213-2600(23)00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. METHODS In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. FINDINGS Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. INTERPRETATION After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification. FUNDING UK Research and Innovation and National Institute for Health Research.
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18
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Zhu Y, Almeida FJ, Baillie JK, Bowen AC, Britton PN, Brizuela ME, Buonsenso D, Burgner D, Chew KY, Chokephaibulkit K, Cohen C, Cormier SA, Crawford N, Curtis N, Farias CGA, Gilks CF, von Gottberg A, Hamer D, Jarovsky D, Jassat W, Jesus AR, Kemp LS, Khumcha B, McCallum G, Miller JE, Morello R, Munro APS, Openshaw PJM, Padmanabhan S, Phongsamart W, Reubenson G, Ritz N, Rodrigues F, Rungmaitree S, Russell F, Sáfadi MAP, Saner C, Semple MG, Prado da Silva DGB, de Sousa LMM, Diogo Moço Souza M, Spann K, Walaza S, Wolter N, Xia Y, Yeoh DK, Zar HJ, Zimmermann P, Short KR. International Pediatric COVID-19 Severity Over the Course of the Pandemic. JAMA Pediatr 2023; 177:1073-1084. [PMID: 37603343 PMCID: PMC10442787 DOI: 10.1001/jamapediatrics.2023.3117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/21/2023] [Indexed: 08/22/2023]
Abstract
Importance Multiple SARS-CoV-2 variants have emerged over the COVID-19 pandemic. The implications for COVID-19 severity in children worldwide are unclear. Objective To determine whether the dominant circulating SARS-CoV-2 variants of concern (VOCs) were associated with differences in COVID-19 severity among hospitalized children. Design, Setting, and Participants Clinical data from hospitalized children and adolescents (younger than 18 years) who were SARS-CoV-2 positive were obtained from 9 countries (Australia, Brazil, Italy, Portugal, South Africa, Switzerland, Thailand, UK, and the US) during 3 different time frames. Time frames 1 (T1), 2 (T2), and 3 (T3) were defined to represent periods of dominance by the ancestral virus, pre-Omicron VOCs, and Omicron, respectively. Age groups for analysis were younger than 6 months, 6 months to younger than 5 years, and 5 to younger than 18 years. Children with an incidental positive test result for SARS-CoV-2 were excluded. Exposures SARS-CoV-2 hospitalization during the stipulated time frame. Main Outcomes and Measures The severity of disease was assessed by admission to intensive care unit (ICU), the need for ventilatory support, or oxygen therapy. Results Among 31 785 hospitalized children and adolescents, the median age was 4 (IQR 1-12) years and 16 639 were male (52.3%). In children younger than 5 years, across successive SARS-CoV-2 waves, there was a reduction in ICU admission (T3 vs T1: risk ratio [RR], 0.56; 95% CI, 0.42-0.75 [younger than 6 months]; RR, 0.61, 95% CI; 0.47-0.79 [6 months to younger than 5 years]), but not ventilatory support or oxygen therapy. In contrast, ICU admission (T3 vs T1: RR, 0.39, 95% CI, 0.32-0.48), ventilatory support (T3 vs T1: RR, 0.37; 95% CI, 0.27-0.51), and oxygen therapy (T3 vs T1: RR, 0.47; 95% CI, 0.32-0.70) decreased across SARS-CoV-2 waves in children 5 years to younger than 18 years old. The results were consistent when data were restricted to unvaccinated children. Conclusions and Relevance This study provides valuable insights into the impact of SARS-CoV-2 VOCs on the severity of COVID-19 in hospitalized children across different age groups and countries, suggesting that while ICU admissions decreased across the pandemic in all age groups, ventilatory and oxygen support generally did not decrease over time in children aged younger than 5 years. These findings highlight the importance of considering different pediatric age groups when assessing disease severity in COVID-19.
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Affiliation(s)
- Yanshan Zhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Flávia Jacqueline Almeida
- Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Asha C Bowen
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, the Children's Hospital, Westmead, New South Wales, Australia
- Sydney Medical School and Sydney Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia
| | | | - Danilo Buonsenso
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - David Burgner
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of General Medicine, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kulkanya Chokephaibulkit
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephania A Cormier
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
- Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | - Nigel Crawford
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of General Medicine, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Nigel Curtis
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Infectious Diseases, The Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
| | - Camila G A Farias
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Charles F Gilks
- School of Public Health, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Diana Hamer
- Our Lady of the Lake Children's Hospital, Baton Rouge, Louisiana
| | - Daniel Jarovsky
- Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Waasila Jassat
- Division of the National Health Laboratory Services, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Ana Rita Jesus
- Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Lisa S Kemp
- Our Lady of the Lake Children's Hospital, Baton Rouge, Louisiana
| | - Benjawan Khumcha
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Georgina McCallum
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jessica E Miller
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Rosa Morello
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Alasdair P S Munro
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust: London, London, United Kingdom
| | - Srivatsan Padmanabhan
- Elson S. Floyd College of Medicine, Washington State University, Tacoma, Washington
- St Joseph Medical Center, Tacoma, Washington
| | - Wanatpreeya Phongsamart
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Gary Reubenson
- Empilweni Service & Research Unit, Rahima Moosa Mother & Child Hospital, Department of Paediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Ritz
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Mycobacterial and Migrant Health Research Group, University of Basel Children's Hospital Basel and Department of Clinical Research, University of Basel, Basel, Switzerland
- Department of Pediatrics and Pediatric Infectious Diseases, Children's Hospital Lucerne and Faculty of Health Science and Medicine, University of Lucerne, Lucerne, Switzerland
| | - Fernanda Rodrigues
- Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Supattra Rungmaitree
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Fiona Russell
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Marco A P Sáfadi
- Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Christoph Saner
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, University Hospital Inselspital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, United Kingdom
| | | | | | | | - Kirsten Spann
- Centre for Immunology and Infection Control, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yao Xia
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel K Yeoh
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Petra Zimmermann
- Department of Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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19
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Roper KJ, Thomas J, Albalawi W, Maddocks E, Dobson S, Alshehri A, Barone FG, Baltazar M, Semple MG, Ho A, Turtle L, Paxton WA, Pollakis G. Quantifying neutralising antibody responses against SARS-CoV-2 in dried blood spots (DBS) and paired sera. Sci Rep 2023; 13:15014. [PMID: 37697014 PMCID: PMC10495436 DOI: 10.1038/s41598-023-41928-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
The ongoing SARS-CoV-2 pandemic was initially managed by non-pharmaceutical interventions such as diagnostic testing, isolation of positive cases, physical distancing and lockdowns. The advent of vaccines has provided crucial protection against SARS-CoV-2. Neutralising antibody (nAb) responses are a key correlate of protection, and therefore measuring nAb responses is essential for monitoring vaccine efficacy. Fingerstick dried blood spots (DBS) are ideal for use in large-scale sero-surveillance because they are inexpensive, offer the option of self-collection and can be transported and stored at ambient temperatures. Such advantages also make DBS appealing to use in resource-limited settings and in potential future pandemics. In this study, nAb responses in sera, venous blood and fingerstick blood stored on filter paper were measured. Samples were collected from SARS-CoV-2 acutely infected individuals, SARS-CoV-2 convalescent individuals and SARS-CoV-2 vaccinated individuals. Good agreement was observed between the nAb responses measured in eluted DBS and paired sera. Stability of nAb responses was also observed in sera stored on filter paper at room temperature for 28 days. Overall, this study provides support for the use of filter paper as a viable sample collection method to study nAb responses.
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Affiliation(s)
- Kelly J Roper
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Wejdan Albalawi
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Emily Maddocks
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Susan Dobson
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Abdullateef Alshehri
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Francesco G Barone
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, L69 3BX, UK
| | - Murielle Baltazar
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Malcolm G Semple
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Lance Turtle
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.
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20
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Pinto Pereira SM, Mensah A, Nugawela MD, Stephenson T, Ladhani SN, Dalrymple E, Dudley J, McOwat K, Simmons R, Heyman I, Segal T, Semple MG, Xu L, Shafran R. Long COVID in Children and Young after Infection or Reinfection with the Omicron Variant: A Prospective Observational Study. J Pediatr 2023; 259:113463. [PMID: 37172813 PMCID: PMC10171900 DOI: 10.1016/j.jpeds.2023.113463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/29/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
To describe the prevalence of long COVID in children infected for the first time (n = 332) or reinfected (n = 243) with Omicron compared with test-negative children (n = 311). Overall, 12%-16% of those infected with Omicron met the research definition of long COVID at 3 and 6 months after infection, with no evidence of difference between cases of first positive and reinfected (Pχ2 = 0.17).
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Affiliation(s)
- Snehal M Pinto Pereira
- Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London, UK.
| | - Anna Mensah
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, London, UK
| | | | | | - Shamez N Ladhani
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, London, UK; Paediatric Infectious Diseases Research Group, St. George's University of London, London, UK
| | - Emma Dalrymple
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Jake Dudley
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Kelsey McOwat
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, London, UK
| | - Ruth Simmons
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, London, UK
| | - Isobel Heyman
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Terry Segal
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Laila Xu
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Roz Shafran
- UCL Great Ormond Street Institute of Child Health, London, UK
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21
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Pinto Pereira SM, Nugawela MD, McOwat K, Dalrymple E, Xu L, Ladhani SN, Simmons R, Chalder T, Swann O, Ford T, Heyman I, Segal T, Semple MG, Rojas NK, Consortium CL, Shafran R, Stephenson T. Symptom Profiles of Children and Young People 12 Months after SARS-CoV-2 Testing: A National Matched Cohort Study (The CLoCk Study). Children (Basel) 2023; 10:1227. [PMID: 37508724 PMCID: PMC10377812 DOI: 10.3390/children10071227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Although 99% of children and young people have been exposed to SARS-CoV-2, the long-term prevalence of post-COVID-19 symptoms in young people is unclear. The aim of this study is to describe symptom profiles 12 months after SARS-CoV-2 testing. METHOD A matched cohort study of a national sample of 20,202 children and young people who took a SARS-CoV-2 PCR test between September 2020 and March 2021. RESULTS 12 months post-index-test, there was a difference in the number of symptoms reported by initial negatives who never tested positive (NN) compared to the other three groups who had at least one positive test (p < 0.001). Similarly, 10.2% of the NN group described five-plus symptoms at 12 months compared to 15.9-24.0% in the other three groups who had at least one positive test. The most common symptoms were tiredness, sleeping difficulties, shortness of breath, and headaches for all four groups. For all these symptoms, the initial test positives with subsequent reports of re-infection had higher prevalences than other positive groups (p < 0.001). Symptom profiles, mental health, well-being, fatigue, and quality of life did not vary by vaccination status. CONCLUSIONS Following the pandemic, many young people, particularly those that have had multiple SARS-CoV-2 positive tests, experience a range of symptoms that warrant consideration and potential investigation and intervention.
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Affiliation(s)
- Snehal M. Pinto Pereira
- Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London WC1E 6BT, UK
| | - Manjula D. Nugawela
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Kelsey McOwat
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Emma Dalrymple
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Laila Xu
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Shamez N. Ladhani
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
- Paediatric Infectious Diseases Research Group, St. George’s University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Ruth Simmons
- Immunisations and Vaccine Preventable Diseases, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Trudie Chalder
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London SE5 8AF, UK
| | - Olivia Swann
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh EH16 4TL, UK
| | - Tamsin Ford
- Department of Psychiatry, Hershel Smith Building Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Isobel Heyman
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Terry Segal
- University College London Hospitals NHS Foundation Trust, London NW1 2PG, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool L12 2AP, UK
| | - Natalia K. Rojas
- Division of Surgery & Interventional Science, Faculty of Medical Sciences, University College London, London WC1E 6BT, UK
| | | | - Roz Shafran
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Terence Stephenson
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
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22
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 619:E61. [PMID: 37433877 PMCID: PMC10371859 DOI: 10.1038/s41586-023-06383-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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23
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Docherty AB, Farrell J, Thorpe M, Egan C, Dunn S, Norman L, Shaw CA, Law A, Leeming G, Norris L, Brooks A, Prodan B, MacLeod R, Baxter R, Morris C, Rennie D, Oosthuyzen W, Semple MG, Baillie JK, Pius R, Seth S, Harrison EM, Lone NI. Patient emergency health-care use before hospital admission for COVID-19 and long-term outcomes in Scotland: a national cohort study. Lancet Digit Health 2023; 5:e446-e457. [PMID: 37391265 PMCID: PMC10306342 DOI: 10.1016/s2589-7500(23)00051-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND It is unclear what effect the pattern of health-care use before admission to hospital with COVID-19 (index admission) has on the long-term outcomes for patients. We sought to describe mortality and emergency readmission to hospital after discharge following the index admission (index discharge), and to assess associations between these outcomes and patterns of health-care use before such admissions. METHODS We did a national, retrospective, complete cohort study by extracting data from several national databases and linking the databases for all adult patients admitted to hospital in Scotland with COVID-19. We used latent class trajectory modelling to identify distinct clusters of patients on the basis of their emergency admissions to hospital in the 2 years before the index admission. The primary outcomes were mortality and emergency readmission up to 1 year after index admission. We used multivariable regression models to explore associations between these outcomes and patient demographics, vaccination status, level of care received in hospital, and previous emergency hospital use. FINDINGS Between March 1, 2020, and Oct 25, 2021, 33 580 patients were admitted to hospital with COVID-19 in Scotland. Overall, the Kaplan-Meier estimate of mortality within 1 year of index admission was 29·6% (95% CI 29·1-30·2). The cumulative incidence of emergency hospital readmission within 30 days of index discharge was 14·4% (95% CI 14·0-14·8), with the number increasing to 35·6% (34·9-36·3) patients at 1 year. Among the 33 580 patients, we identified four distinct patterns of previous emergency hospital use: no admissions (n=18 772 [55·9%]); minimal admissions (n=12 057 [35·9%]); recently high admissions (n=1931 [5·8%]), and persistently high admissions (n=820 [2·4%]). Patients with recently or persistently high admissions were older, more multimorbid, and more likely to have hospital-acquired COVID-19 than patients with no or minimal admissions. People in the minimal, recently high, and persistently high admissions groups had an increased risk of mortality and hospital readmission compared with those in the no admissions group. Compared with the no admissions group, mortality was highest in the recently high admissions group (post-hospital mortality HR 2·70 [95% CI 2·35-2·81]; p<0·0001) and the risk of readmission was highest in the persistently high admissions group (3·23 [2·89-3·61]; p<0·0001). INTERPRETATION Long-term mortality and readmission rates for patients hospitalised with COVID-19 were high; within 1 year, one in three patients had died and a third had been readmitted as an emergency. Patterns of hospital use before index admission were strongly predictive of mortality and readmission risk, independent of age, pre-existing comorbidities, and COVID-19 vaccination status. This increasingly precise identification of individuals at high risk of poor outcomes from COVID-19 will enable targeted support. FUNDING Chief Scientist Office Scotland, UK National Institute for Health Research, and UK Research and Innovation.
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Affiliation(s)
- Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - James Farrell
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Mathew Thorpe
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Conor Egan
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Sarah Dunn
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Lisa Norman
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Catherine A Shaw
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gary Leeming
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Lucy Norris
- Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Andrew Brooks
- Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Bianca Prodan
- Bayes Centre, University of Edinburgh, Edinburgh, UK
| | | | - Robert Baxter
- Bayes Centre, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - Riinu Pius
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Sohan Seth
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Nazir I Lone
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
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24
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Yang H, Sun H, Brackenridge S, Zhuang X, Wing PAC, Quastel M, Walters L, Garner L, Wang B, Yao X, Felce SL, Peng Y, Moore S, Peeters BWA, Rei M, Canto Gomes J, Tomas A, Davidson A, Semple MG, Turtle LCW, Openshaw PJM, Baillie JK, Mentzer AJ, Klenerman P, Borrow P, Dong T, McKeating JA, Gillespie GM, McMichael AJ. HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation. Sci Immunol 2023; 8:eabl8881. [PMID: 37390223 DOI: 10.1126/sciimmunol.abl8881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Pathogen-specific CD8+ T cell responses restricted by the nonpolymorphic nonclassical class Ib molecule human leukocyte antigen E (HLA-E) are rarely reported in viral infections. The natural HLA-E ligand is a signal peptide derived from classical class Ia HLA molecules that interact with the NKG2/CD94 receptors to regulate natural killer cell functions, but pathogen-derived peptides can also be presented by HLA-E. Here, we describe five peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that elicited HLA-E-restricted CD8+ T cell responses in convalescent patients with coronavirus disease 2019. These T cell responses were identified in the blood at frequencies similar to those reported for classical HLA-Ia-restricted anti-SARS-CoV-2 CD8+ T cells. HLA-E peptide-specific CD8+ T cell clones, which expressed diverse T cell receptors, suppressed SARS-CoV-2 replication in Calu-3 human lung epithelial cells. SARS-CoV-2 infection markedly down-regulated classical HLA class I expression in Calu-3 cells and primary reconstituted human airway epithelial cells, whereas HLA-E expression was not affected, enabling T cell recognition. Thus, HLA-E-restricted T cells could contribute to the control of SARS-CoV-2 infection alongside classical T cells.
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Affiliation(s)
- Hongbing Yang
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Hong Sun
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Key Laboratory of AIDS Immunology, Department of Laboratory Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Simon Brackenridge
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Peter A C Wing
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lucy Walters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lee Garner
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Beibei Wang
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Shona Moore
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bas W A Peeters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Oxford, UK
| | - Joao Canto Gomes
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal
| | - Ana Tomas
- Unidada de Investigacao em Patobiologia Molecular, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, EPE Lisbon, Portugal
- Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Unit, Alder Hey Children's Hospital, Eaton Road, Liverpool L12 2AP, UK
| | - Lance C W Turtle
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), Liverpool, UK
| | | | | | - Alexander J Mentzer
- Welcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jane A McKeating
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
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25
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Pauley E, Drake TM, Griffith DM, Sigfrid L, Lone NI, Harrison EM, Baillie JK, Scott JT, Walsh TS, Semple MG, Docherty AB. Recovery from Covid-19 critical illness: A secondary analysis of the ISARIC4C CCP-UK cohort study and the RECOVER trial. J Intensive Care Soc 2023; 24:162-169. [PMID: 37255989 PMCID: PMC10225805 DOI: 10.1177/17511437211052226] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Background We aimed to compare the prevalence and severity of fatigue in survivors of Covid-19 versus non-Covid-19 critical illness, and to explore potential associations between baseline characteristics and worse recovery. Methods We conducted a secondary analysis of two prospectively collected datasets. The population included was 92 patients who received invasive mechanical ventilation (IMV) with Covid-19, and 240 patients who received IMV with non-Covid-19 illness before the pandemic. Follow-up data were collected post-hospital discharge using self-reported questionnaires. The main outcome measures were self-reported fatigue severity and the prevalence of severe fatigue (severity >7/10) 3 and 12-months post-hospital discharge. Results Covid-19 IMV-patients were significantly younger with less prior comorbidity, and more males, than pre-pandemic IMV-patients. At 3-months, the prevalence (38.9% [7/18] vs. 27.1% [51/188]) and severity (median 5.5/10 vs 5.0/10) of fatigue were similar between the Covid-19 and pre-pandemic populations, respectively. At 6-months, the prevalence (10.3% [3/29] vs. 32.5% [54/166]) and severity (median 2.0/10 vs. 5.7/10) of fatigue were less in the Covid-19 cohort. In the total sample of IMV-patients included (i.e. all Covid-19 and pre-pandemic patients), having Covid-19 was significantly associated with less severe fatigue (severity <7/10) after adjusting for age, sex and prior comorbidity (adjusted OR 0.35 (95%CI 0.15-0.76, p=0.01). Conclusion Fatigue may be less severe after Covid-19 than after other critical illness.
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Affiliation(s)
- Ellen Pauley
- , Edinburgh, UKUniversity of Edinburgh Medical School
| | - Thomas M Drake
- Centre for Medical Informatics, The Usher Institute, , Edinburgh, UKUniversity of Edinburgh
| | - David M Griffith
- Anaesthesia, Critical Care and Pain Medicine, , Edinburgh, UKUniversity of Edinburgh
| | - Louise Sigfrid
- Centre for Tropical Medicine and Global Health, , Oxford, UKUniversity of Oxford
| | - Nazir I Lone
- Anaesthesia, Critical Care and Pain Medicine, , Edinburgh, UKUniversity of Edinburgh
- Centre for Population Health Sciences, The Usher Institute, , Edinburgh, UKUniversity of Edinburgh
| | - Ewen M Harrison
- Centre for Medical Informatics, The Usher Institute, , Edinburgh, UKUniversity of Edinburgh
| | - J Kenneth Baillie
- Anaesthesia, Critical Care and Pain Medicine, , Edinburgh, UKUniversity of Edinburgh
- Roslin Institute, , Edinburgh, UKUniversity of Edinburgh
| | - Janet T Scott
- , Glasgow, UKMRC-University of Glasgow Centre for Virus Research
| | - Timothy S Walsh
- Anaesthesia, Critical Care and Pain Medicine, , Edinburgh, UKUniversity of Edinburgh
| | - Malcolm G Semple
- NIHR Health Protection Unit in Emerging Infectious Diseases, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, , Liverpool, UKUniversity of Liverpool
| | - Annemarie B Docherty
- Centre for Medical Informatics, The Usher Institute, , Edinburgh, UKUniversity of Edinburgh
- Anaesthesia, Critical Care and Pain Medicine, , Edinburgh, UKUniversity of Edinburgh
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26
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Ho A, Orton R, Tayler R, Asamaphan P, Herder V, Davis C, Tong L, Smollett K, Manali M, Allan J, Rawlik K, McDonald SE, Vink E, Pollock L, Gannon L, Evans C, McMenamin J, Roy K, Marsh K, Divala T, Holden MTG, Lockhart M, Yirrell D, Currie S, O'Leary M, Henderson D, Shepherd SJ, Jackson C, Gunson R, MacLean A, McInnes N, Bradley-Stewart A, Battle R, Hollenbach JA, Henderson P, Odam M, Chikowore P, Oosthuyzen W, Chand M, Hamilton MS, Estrada-Rivadeneyra D, Levin M, Avramidis N, Pairo-Castineira E, Vitart V, Wilkie C, Palmarini M, Ray S, Robertson DL, da Silva Filipe A, Willett BJ, Breuer J, Semple MG, Turner D, Baillie JK, Thomson EC. Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature 2023; 617:555-563. [PMID: 36996873 DOI: 10.1038/s41586-023-05948-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/10/2023] [Indexed: 04/01/2023]
Abstract
An outbreak of acute hepatitis of unknown aetiology in children was reported in Scotland1 in April 2022 and has now been identified in 35 countries2. Several recent studies have suggested an association with human adenovirus with this outbreak, a virus not commonly associated with hepatitis. Here we report a detailed case-control investigation and find an association between adeno-associated virus 2 (AAV2) infection and host genetics in disease susceptibility. Using next-generation sequencing, PCR with reverse transcription, serology and in situ hybridization, we detected recent infection with AAV2 in plasma and liver samples in 26 out of 32 (81%) cases of hepatitis compared with 5 out of 74 (7%) of samples from unaffected individuals. Furthermore, AAV2 was detected within ballooned hepatocytes alongside a prominent T cell infiltrate in liver biopsy samples. In keeping with a CD4+ T-cell-mediated immune pathology, the human leukocyte antigen (HLA) class II HLA-DRB1*04:01 allele was identified in 25 out of 27 cases (93%) compared with a background frequency of 10 out of 64 (16%; P = 5.49 × 10-12). In summary, we report an outbreak of acute paediatric hepatitis associated with AAV2 infection (most likely acquired as a co-infection with human adenovirus that is usually required as a 'helper virus' to support AAV2 replication) and disease susceptibility related to HLA class II status.
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Affiliation(s)
- Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Richard Orton
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Rachel Tayler
- Department of Paediatrics, Royal Hospital for Children, Glasgow, UK
| | - Patawee Asamaphan
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Vanessa Herder
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Chris Davis
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lily Tong
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Katherine Smollett
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Maria Manali
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jay Allan
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Konrad Rawlik
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Sarah E McDonald
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Elen Vink
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Louisa Pollock
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
- Department of Paediatrics, Royal Hospital for Children, Glasgow, UK
| | | | - Clair Evans
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Celia Jackson
- West of Scotland Specialist Virology Centre, Glasgow, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow, UK
| | | | - Neil McInnes
- West of Scotland Specialist Virology Centre, Glasgow, UK
| | | | - Richard Battle
- Histocompatibility and Immunogenetics (H&I) Laboratory, Scottish National Blood Transfusion Service, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Jill A Hollenbach
- Department of Neurology and Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Henderson
- Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Miranda Odam
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Primrose Chikowore
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Melissa Shea Hamilton
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Diego Estrada-Rivadeneyra
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Nikos Avramidis
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Erola Pairo-Castineira
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Veronique Vitart
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - David L Robertson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Ana da Silva Filipe
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Brian J Willett
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | - David Turner
- Histocompatibility and Immunogenetics (H&I) Laboratory, Scottish National Blood Transfusion Service, Edinburgh Royal Infirmary, Edinburgh, UK
| | - J Kenneth Baillie
- Pandemic Science Hub, Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Emma C Thomson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK.
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK.
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27
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Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature 2023; 617:764-768. [PMID: 37198478 PMCID: PMC10208981 DOI: 10.1038/s41586-023-06034-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/27/2023] [Indexed: 05/19/2023]
Abstract
Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown1 to be highly efficient for discovery of genetic associations2. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group3. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).
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Affiliation(s)
- Erola Pairo-Castineira
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew D Bretherick
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Pain Service, NHS Tayside, Ninewells Hospital and Medical School, Dundee, UK
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Marie Zechner
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Fiona Griffiths
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Wilna Oosthuyzen
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jonathan Millar
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Clark D Russell
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ryan Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Manu Shankar-Hari
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Charles Hinds
- William Harvey Research Institute Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Colin Begg
- Royal Hospital for Children, Glasgow, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Malak Abedalthagafi
- Genomic Research Department, King Fahad Medical City, Riyadh, Saudi Arabia
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Andre D Luchessi
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Raquel Cruz
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) Santiago de Compostela, Santiago de Compostela, Spain
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Fairfax
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Clohisey Hendry
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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28
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Kartsonaki C, Baillie JK, Barrio NG, Baruch J, Beane A, Blumberg L, Bozza F, Broadley T, Burrell A, Carson G, Citarella BW, Dagens A, Dankwa EA, Donnelly CA, Dunning J, Elotmani L, Escher M, Farshait N, Goffard JC, Gonçalves BP, Hall M, Hashmi M, Sim Lim Heng B, Ho A, Jassat W, Pedrera Jiménez M, Laouenan C, Lissauer S, Martin-Loeches I, Mentré F, Merson L, Morton B, Munblit D, Nekliudov NA, Nichol AD, Singh Oinam BC, Ong D, Panda PK, Petrovic M, Pritchard MG, Ramakrishnan N, Ramos GV, Roger C, Sandulescu O, Semple MG, Sharma P, Sigfrid L, Somers EC, Streinu-Cercel A, Taccone F, Vecham PK, Kumar Tirupakuzhi Vijayaraghavan B, Wei J, Wils EJ, Ci Wong X, Horby P, Rojek A, Olliaro PL. Characteristics and outcomes of an international cohort of 600 000 hospitalized patients with COVID-19. Int J Epidemiol 2023; 52:355-376. [PMID: 36850054 PMCID: PMC10114094 DOI: 10.1093/ije/dyad012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/01/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND We describe demographic features, treatments and clinical outcomes in the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) COVID-19 cohort, one of the world's largest international, standardized data sets concerning hospitalized patients. METHODS The data set analysed includes COVID-19 patients hospitalized between January 2020 and January 2022 in 52 countries. We investigated how symptoms on admission, co-morbidities, risk factors and treatments varied by age, sex and other characteristics. We used Cox regression models to investigate associations between demographics, symptoms, co-morbidities and other factors with risk of death, admission to an intensive care unit (ICU) and invasive mechanical ventilation (IMV). RESULTS Data were available for 689 572 patients with laboratory-confirmed (91.1%) or clinically diagnosed (8.9%) SARS-CoV-2 infection from 52 countries. Age [adjusted hazard ratio per 10 years 1.49 (95% CI 1.48, 1.49)] and male sex [1.23 (1.21, 1.24)] were associated with a higher risk of death. Rates of admission to an ICU and use of IMV increased with age up to age 60 years then dropped. Symptoms, co-morbidities and treatments varied by age and had varied associations with clinical outcomes. The case-fatality ratio varied by country partly due to differences in the clinical characteristics of recruited patients and was on average 21.5%. CONCLUSIONS Age was the strongest determinant of risk of death, with a ∼30-fold difference between the oldest and youngest groups; each of the co-morbidities included was associated with up to an almost 2-fold increase in risk. Smoking and obesity were also associated with a higher risk of death. The size of our international database and the standardized data collection method make this study a comprehensive international description of COVID-19 clinical features. Our findings may inform strategies that involve prioritization of patients hospitalized with COVID-19 who have a higher risk of death.
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Affiliation(s)
- Christiana Kartsonaki
- Medical Research Council (MRC) Population Health Research Unit, Clinical Trials Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Joaquín Baruch
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Lucille Blumberg
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Fernando Bozza
- National Institute of Infectious Disease Evandro Chagas, Oswaldo Cruz Foundation (INI-FIOCRUZ), Ministry of Health, and D'Or Institute of Research and Education (IDOR), Rio de Janeiro, São Paulo, Brazil
| | | | | | - Gail Carson
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Barbara Wanjiru Citarella
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Dagens
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christl A Donnelly
- Department of Statistics, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jake Dunning
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Martina Escher
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Bronner P Gonçalves
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Madiha Hashmi
- Critical Care Asia and Ziauddin University, Karachi, Pakistan
| | | | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK
| | - Waasila Jassat
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Cedric Laouenan
- Université de Paris, France, Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, Paris, France
| | | | | | - France Mentré
- Université de Paris, France, Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, Paris, France
| | - Laura Merson
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Ben Morton
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Daniel Munblit
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child’s Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Alistair D Nichol
- Irish Critical Care Critical Clinical Trials Network, Dublin, Ireland
| | | | - David Ong
- Franciscus Gasthuis & Vlietland, Rotterdam, Netherlands
| | | | | | - Mark G Pritchard
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Grazielle Viana Ramos
- National Institute of Infectious Disease Evandro Chagas, Oswaldo Cruz Foundation (INI-FIOCRUZ), Ministry of Health, and D'Or Institute of Research and Education (IDOR), Rio de Janeiro, São Paulo, Brazil
| | | | - Oana Sandulescu
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases ‘Prof. Dr. Matei Bals’, Bucharest, Romania
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- UK Respiratory Medicine, Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Pratima Sharma
- University of Michigan Schools of Medicine & Public Health, Ann Arbor, Michigan, USA
| | - Louise Sigfrid
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emily C Somers
- University of Michigan Schools of Medicine & Public Health, Ann Arbor, Michigan, USA
| | | | - Fabio Taccone
- Cliniques Universitaires de Bruxelles (CUB) Hopital Erasme, Anderlecht, Belgium
| | | | | | - Jia Wei
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Xin Ci Wong
- National Institutes of Health (NIH), Ministry of Health, Shah Alam, Malaysia
| | - Peter Horby
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amanda Rojek
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Royal Melbourne Hospital, Melbourne, Australia
- Centre for Integrated Critical Care, University of Melbourne, Melbourne, Australia
| | - Piero L Olliaro
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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29
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Keogh RH, Diaz-Ordaz K, Jewell NP, Semple MG, de Wreede LC, Putter H. Estimating distribution of length of stay in a multi-state model conditional on the pathway, with an application to patients hospitalised with Covid-19. Lifetime Data Anal 2023; 29:288-317. [PMID: 36754952 PMCID: PMC9908509 DOI: 10.1007/s10985-022-09586-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/12/2022] [Indexed: 05/27/2023]
Abstract
Multi-state models are used to describe how individuals transition through different states over time. The distribution of the time spent in different states, referred to as 'length of stay', is often of interest. Methods for estimating expected length of stay in a given state are well established. The focus of this paper is on the distribution of the time spent in different states conditional on the complete pathway taken through the states, which we call 'conditional length of stay'. This work is motivated by questions about length of stay in hospital wards and intensive care units among patients hospitalised due to Covid-19. Conditional length of stay estimates are useful as a way of summarising individuals' transitions through the multi-state model, and also as inputs to mathematical models used in planning hospital capacity requirements. We describe non-parametric methods for estimating conditional length of stay distributions in a multi-state model in the presence of censoring, including conditional expected length of stay (CELOS). Methods are described for an illness-death model and then for the more complex motivating example. The methods are assessed using a simulation study and shown to give unbiased estimates of CELOS, whereas naive estimates of CELOS based on empirical averages are biased in the presence of censoring. The methods are applied to estimate conditional length of stay distributions for individuals hospitalised due to Covid-19 in the UK, using data on 42,980 individuals hospitalised from March to July 2020 from the COVID19 Clinical Information Network.
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Affiliation(s)
- Ruth H Keogh
- Department of Medical Statistics and Centre for Statistical Methodology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Karla Diaz-Ordaz
- Department of Medical Statistics and Centre for Statistical Methodology, London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas P Jewell
- Department of Medical Statistics and Centre for Statistical Methodology, London School of Hygiene and Tropical Medicine, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | | | - Hein Putter
- Leiden University Medical Center, Leiden, Netherlands
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30
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Stewart I, Jacob J, George PM, Molyneaux PL, Porter JC, Allen RJ, Aslani S, Baillie JK, Barratt SL, Beirne P, Bianchi SM, Blaikley JF, Chalmers JD, Chambers RC, Chadhuri N, Coleman C, Collier G, Denneny EK, Docherty A, Elneima O, Evans RA, Fabbri L, Gibbons MA, Gleeson FV, Gooptu B, Greening NJ, Guio BG, Hall IP, Hanley NA, Harris V, Harrison EM, Heightman M, Hillman TE, Horsley A, Houchen-Wolloff L, Jarrold I, Johnson SR, Jones MG, Khan F, Lawson R, Leavy O, Lone N, Marks M, McAuley H, Mehta P, Parekh D, Hanley KP, Platé M, Pearl J, Poinasamy K, Quint JK, Raman B, Richardson M, Rivera-Ortega P, Saunders L, Saunders R, Semple MG, Sereno M, Shikotra A, Simpson AJ, Singapuri A, Smith DJF, Spears M, Spencer LG, Stanel S, Thickett DR, Thompson AAR, Thorpe M, Walsh SLF, Walker S, Weatherley ND, Weeks ME, Wild JM, Wootton DG, Brightling CE, Ho LP, Wain LV, Jenkins GR. Residual Lung Abnormalities after COVID-19 Hospitalization: Interim Analysis of the UKILD Post-COVID-19 Study. Am J Respir Crit Care Med 2023; 207:693-703. [PMID: 36457159 PMCID: PMC10037479 DOI: 10.1164/rccm.202203-0564oc] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/01/2022] [Indexed: 12/04/2022] Open
Abstract
Rationale: Shared symptoms and genetic architecture between coronavirus disease (COVID-19) and lung fibrosis suggest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may lead to progressive lung damage. Objectives: The UK Interstitial Lung Disease Consortium (UKILD) post-COVID-19 study interim analysis was planned to estimate the prevalence of residual lung abnormalities in people hospitalized with COVID-19 on the basis of risk strata. Methods: The PHOSP-COVID-19 (Post-Hospitalization COVID-19) study was used to capture routine and research follow-up within 240 days from discharge. Thoracic computed tomography linked by PHOSP-COVID-19 identifiers was scored for the percentage of residual lung abnormalities (ground-glass opacities and reticulations). Risk factors in linked computed tomography were estimated with Bayesian binomial regression, and risk strata were generated. Numbers within strata were used to estimate posthospitalization prevalence using Bayesian binomial distributions. Sensitivity analysis was restricted to participants with protocol-driven research follow-up. Measurements and Main Results: The interim cohort comprised 3,700 people. Of 209 subjects with linked computed tomography (median, 119 d; interquartile range, 83-155), 166 people (79.4%) had more than 10% involvement of residual lung abnormalities. Risk factors included abnormal chest X-ray (risk ratio [RR], 1.21; 95% credible interval [CrI], 1.05-1.40), percent predicted DlCO less than 80% (RR, 1.25; 95% CrI, 1.00-1.56), and severe admission requiring ventilation support (RR, 1.27; 95% CrI, 1.07-1.55). In the remaining 3,491 people, moderate to very high risk of residual lung abnormalities was classified at 7.8%, and posthospitalization prevalence was estimated at 8.5% (95% CrI, 7.6-9.5), rising to 11.7% (95% CrI, 10.3-13.1) in the sensitivity analysis. Conclusions: Residual lung abnormalities were estimated in up to 11% of people discharged after COVID-19-related hospitalization. Health services should monitor at-risk individuals to elucidate long-term functional implications.
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Affiliation(s)
- Iain Stewart
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | | | - Peter M. George
- Royal Brompton and Harefield Clinical Group, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Philip L. Molyneaux
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | | | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | | | | | | | - Paul Beirne
- Leeds Teaching Hospitals NHS Foundation Trust, Leeds, United Kingdom
| | - Stephen M. Bianchi
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | | | | | | | | | | | | | | | | | - Omer Elneima
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Rachael A. Evans
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Laura Fabbri
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | | | - Fergus V. Gleeson
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Bibek Gooptu
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Neil J. Greening
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Beatriz Guillen Guio
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Ian P. Hall
- University of Nottingham, Nottingham, United Kingdom
| | | | - Victoria Harris
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | | | | | | | - Alex Horsley
- University of Manchester, Manchester, United Kingdom
| | | | | | | | - Mark G. Jones
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Fasihul Khan
- University of Nottingham, Nottingham, United Kingdom
| | - Rod Lawson
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Olivia Leavy
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Michael Marks
- University College London Hospital, London, United Kingdom
| | - Hamish McAuley
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Puja Mehta
- University College London Hospital, London, United Kingdom
| | - Dhruv Parekh
- University of Birmingham, Brimingham, United Kingdom
| | - Karen Piper Hanley
- University of Manchester, Manchester, United Kingdom
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Manuela Platé
- University College London Hospital, London, United Kingdom
| | - John Pearl
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Jennifer K. Quint
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Betty Raman
- University of Oxford, Oxford, United Kingdom
| | | | | | | | - Ruth Saunders
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | | | - Marco Sereno
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Aarti Shikotra
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | | | - Amisha Singapuri
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - David J. F. Smith
- Royal Brompton and Harefield Clinical Group, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Mark Spears
- Perth Royal Infirmary, NHS Tayside, Perth, United Kingdom; and
| | - Lisa G. Spencer
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Stefan Stanel
- University of Manchester, Manchester, United Kingdom
| | | | | | | | - Simon L. F. Walsh
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | | | | | - Mark E. Weeks
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Jim M. Wild
- University of Sheffield, Sheffield, United Kingdom
| | | | | | - Ling-Pei Ho
- University of Oxford, Oxford, United Kingdom
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Gisli R. Jenkins
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
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31
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Parker E, Thomas J, Roper KJ, Ijaz S, Edwards T, Marchesin F, Katsanovskaja K, Lett L, Jones C, Hardwick HE, Davis C, Vink E, McDonald SE, Moore SC, Dicks S, Jegatheesan K, Cook NJ, Hope J, Cherepanov P, McClure MO, Baillie JK, Openshaw PJM, Turtle L, Ho A, Semple MG, Paxton WA, Tedder RS, Pollakis G. SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study. Front Immunol 2023; 14:1146702. [PMID: 37056776 PMCID: PMC10087108 DOI: 10.3389/fimmu.2023.1146702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured via DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.
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Affiliation(s)
- Eleanor Parker
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jordan Thomas
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kelly J. Roper
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Samreen Ijaz
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, London, United Kingdom
| | - Tansy Edwards
- Medical Research Council (MRC) International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Federica Marchesin
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ksenia Katsanovskaja
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lauren Lett
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Christopher Jones
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hayley E. Hardwick
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Chris Davis
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Elen Vink
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sarah E. McDonald
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shona C. Moore
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Steve Dicks
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, London, United Kingdom
- National Health Service (NHS) Blood and Transplant, London, United Kingdom
| | - Keerthana Jegatheesan
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, London, United Kingdom
- National Health Service (NHS) Blood and Transplant, London, United Kingdom
| | - Nicola J. Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Joshua Hope
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Myra O. McClure
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | | | - Lance Turtle
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Antonia Ho
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Malcolm G. Semple
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - William A. Paxton
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Richard S. Tedder
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Georgios Pollakis
- National Institute of Health and Care Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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32
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Turtle L, Thorpe M, Drake TM, Swets M, Palmieri C, Russell CD, Ho A, Aston S, Wootton DG, Richter A, de Silva TI, Hardwick HE, Leeming G, Law A, Openshaw PJM, Harrison EM, Baillie JK, Semple MG, Docherty AB. Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study. PLoS Med 2023; 20:e1004086. [PMID: 36719907 PMCID: PMC9928075 DOI: 10.1371/journal.pmed.1004086] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/14/2023] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic. METHODS AND FINDINGS We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent. CONCLUSIONS Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group. TRIAL REGISTRATION ISRCTN 66726260.
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Affiliation(s)
- Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Mathew Thorpe
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas M. Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Maaike Swets
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden University, Leiden, the Netherlands
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, United Kingdom
| | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Clark D. Russell
- University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, Edinburgh, United Kingdom
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Stephen Aston
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Daniel G. Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Alex Richter
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Thushan I. de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, The University of Sheffield, Sheffield, United Kingdom
| | - Hayley E. Hardwick
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Gary Leeming
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Andy Law
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ewen M. Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - J. Kenneth Baillie
- The Roslin Institute, Easter Bush campus, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, United Kingdom
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Annemarie B. Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, United Kingdom
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33
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Swann OV, Pollock L, Holden KA, Munro APS, Bennett A, Williams TC, Turtle L, Fairfield CJ, Drake TM, Faust SN, Sinha IP, Roland D, Whittaker E, Ladhani SN, Nguyen-Van-Tam JS, Girvan M, Donohue C, Donegan C, Spencer RG, Hardwick HE, Openshaw PJM, Baillie JK, Harrison EM, Docherty AB, Semple MG. Comparison of UK paediatric SARS-CoV-2 admissions across the first and second pandemic waves. Pediatr Res 2023; 93:207-216. [PMID: 35449394 PMCID: PMC9876790 DOI: 10.1038/s41390-022-02052-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 01/29/2023]
Abstract
BACKGROUND We hypothesised that the clinical characteristics of hospitalised children and young people (CYP) with SARS-CoV-2 in the UK second wave (W2) would differ from the first wave (W1) due to the alpha variant (B.1.1.7), school reopening and relaxation of shielding. METHODS Prospective multicentre observational cohort study of patients <19 years hospitalised in the UK with SARS-CoV-2 between 17/01/20 and 31/01/21. Clinical characteristics were compared between W1 and W2 (W1 = 17/01/20-31/07/20,W2 = 01/08/20-31/01/21). RESULTS 2044 CYP < 19 years from 187 hospitals. 427/2044 (20.6%) with asymptomatic/incidental SARS-CoV-2 were excluded from main analysis. 16.0% (248/1548) of symptomatic CYP were admitted to critical care and 0.8% (12/1504) died. 5.6% (91/1617) of symptomatic CYP had Multisystem Inflammatory Syndrome in Children (MIS-C). After excluding CYP with MIS-C, patients in W2 had lower Paediatric Early Warning Scores (PEWS, composite vital sign score), lower antibiotic use and less respiratory and cardiovascular support than W1. The proportion of CYP admitted to critical care was unchanged. 58.0% (938/1617) of symptomatic CYP had no reported comorbidity. Patients without co-morbidities were younger (42.4%, 398/938, <1 year), had lower PEWS, shorter length of stay and less respiratory support. CONCLUSIONS We found no evidence of increased disease severity in W2 vs W1. A large proportion of hospitalised CYP had no comorbidity. IMPACT No evidence of increased severity of COVID-19 admissions amongst children and young people (CYP) in the second vs first wave in the UK, despite changes in variant, relaxation of shielding and return to face-to-face schooling. CYP with no comorbidities made up a significant proportion of those admitted. However, they had shorter length of stays and lower treatment requirements than CYP with comorbidities once those with MIS-C were excluded. At least 20% of CYP admitted in this cohort had asymptomatic/incidental SARS-CoV-2 infection. This paper was presented to SAGE to inform CYP vaccination policy in the UK.
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Affiliation(s)
- Olivia V Swann
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
- Paediatric Infectious Diseases, Royal Hospital for Children, Glasgow, UK
| | - Louisa Pollock
- Paediatric Infectious Diseases, Royal Hospital for Children, Glasgow, UK
- Child Health, School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow, UK
| | - Karl A Holden
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Alasdair P S Munro
- NIHR Southampton Clinical Research Facility and NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Aisleen Bennett
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | - Thomas C Williams
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- Tropical and Infectious Diseases Unit, Liverpool University Hospitals NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Saul N Faust
- NIHR Southampton Clinical Research Facility and NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Ian P Sinha
- Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
- Women's and Children's Health, Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Damian Roland
- Paediatric Emergency Medicine Leicester Academic (PEMLA) Group, University Hospitals of Leicester NHS Trust, Leicester, UK
- SAPPHIRE Group, Health Sciences, Leicester University, Leicester, UK
| | - Elizabeth Whittaker
- Section of Paediatric Infectious Diseases, Imperial College London, London, UK
- Paediatric Infectious Diseases, Imperial College Healthcare National Health System Trust, London, UK
| | - Shamez N Ladhani
- Immunisation and Countermeasures Division, Public Health England Colindale, London, UK
- Paediatric Infectious Disease, St. George's Hospital London, London, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK
| | - Michelle Girvan
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Chloe Donohue
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Cara Donegan
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Rebecca G Spencer
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Hayley E Hardwick
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK.
- Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK.
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Hughes DM, Cheyne CP, Ashton M, Coffey E, Crozier A, Semple MG, Buchan I, García-Fiñana M. Association of SARS-CoV-2 viral load distributions with individual demographics and suspected variant type: results from the Liverpool community testing pilot, England, 6 November 2020 to 8 September 2021. Euro Surveill 2023; 28:2200129. [PMID: 36700865 PMCID: PMC9881177 DOI: 10.2807/1560-7917.es.2023.28.4.2200129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BackgroundThe PCR quantification cycle (Cq) is a proxy measure of the viral load of a SARS-CoV-2-infected individual.AimTo investigate if Cq values vary according to different population characteristics, in particular demographic ones, and within the COVID-19 pandemic context, notably the SARS-CoV-2 type/variant individuals get infected with.MethodsWe considered all positive PCR results from Cheshire and Merseyside, England, between 6 November 2020 and 8 September 2021. Cq distributions were inspected with Kernel density estimates. Multivariable quantile regression models assessed associations between people's features and Cq.ResultsWe report Cq values for 188,821 SARS-CoV-2 positive individuals. Median Cqs increased with decreasing age for suspected wild-type virus and Alpha variant infections, but less so, if not, for Delta. For example, compared to 30-39-year-olds (median age group), 5-11-year-olds exhibited 1.8 (95% CI: 1.5 to 2.1), 2.2 (95% CI: 1.8 to 2.6) and 0.8 (95% CI: 0.6 to 0.9) higher median Cqs for suspected wild-type, Alpha and Delta positives, respectively, in multivariable analysis. 12-18-year-olds also had higher Cqs for wild-type and Alpha positives, however, not for Delta. Overall, in univariable analysis, suspected Delta positives reported 2.8 lower median Cqs than wild-type positives (95% CI: 2.7 to 2.8; p < 0.001). Suspected Alpha positives had 1.5 (95% CI: 1.4 to 1.5; p < 0.001) lower median Cqs than wild type.ConclusionsWild-type- or Alpha-infected school-aged children (5-11-year-olds) might transmit less than adults (> 18 years old), but have greater mixing exposures. Smaller differences in viral loads with age occurred in suspected Delta infections. Suspected-Alpha- or Delta-infections involved higher viral loads than wild type, suggesting increased transmission risk. COVID-19 control strategies should consider age and dominant variant.
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Affiliation(s)
- David M Hughes
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
| | - Christopher P Cheyne
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
| | - Matthew Ashton
- Department of Public Health, Liverpool City Council, Liverpool, United Kingdom
| | - Emer Coffey
- Department of Public Health, Liverpool City Council, Liverpool, United Kingdom
| | - Alex Crozier
- Division of biosciences, University College London, London, United Kingdom
| | - Malcolm G Semple
- Health Protection Research Unity in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, United Kingdom
| | - Iain Buchan
- Department of Public Health, Policy and Systems, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
| | - Marta García-Fiñana
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, United Kingdom
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Liew F, Talwar S, Cross A, Willett BJ, Scott S, Logan N, Siggins MK, Swieboda D, Sidhu JK, Efstathiou C, Moore SC, Davis C, Mohamed N, Nunag J, King C, Thompson AAR, Rowland-Jones SL, Docherty AB, Chalmers JD, Ho LP, Horsley A, Raman B, Poinasamy K, Marks M, Kon OM, Howard L, Wootton DG, Dunachie S, Quint JK, Evans RA, Wain LV, Fontanella S, de Silva TI, Ho A, Harrison E, Baillie JK, Semple MG, Brightling C, Thwaites RS, Turtle L, Openshaw PJM. SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination. EBioMedicine 2023; 87:104402. [PMID: 36543718 PMCID: PMC9762734 DOI: 10.1016/j.ebiom.2022.104402] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript.
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Affiliation(s)
- Felicity Liew
- National Heart and Lung Institute, Imperial College London, UK.
| | - Shubha Talwar
- National Heart and Lung Institute, Imperial College London, UK
| | - Andy Cross
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, Immunity and Inflammation, University of Glasgow, UK
| | - Sam Scott
- MRC-University of Glasgow Centre for Virus Research, Immunity and Inflammation, University of Glasgow, UK
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, Immunity and Inflammation, University of Glasgow, UK
| | | | - Dawid Swieboda
- National Heart and Lung Institute, Imperial College London, UK
| | - Jasmin K Sidhu
- National Heart and Lung Institute, Imperial College London, UK
| | | | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Immunity and Inflammation, University of Glasgow, UK
| | - Noura Mohamed
- Cardiovascular Research Team, Imperial College Healthcare NHS Trust, London, UK
| | - Jose Nunag
- Cardiovascular Research Team, Imperial College Healthcare NHS Trust, London, UK
| | - Clara King
- Cardiovascular Research Team, Imperial College Healthcare NHS Trust, London, UK
| | - A A Roger Thompson
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Sarah L Rowland-Jones
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - James D Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | - Alexander Horsley
- Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Betty Raman
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Michael Marks
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Onn Min Kon
- National Heart and Lung Institute, Imperial College London, UK
| | - Luke Howard
- National Heart and Lung Institute, Imperial College London, UK
| | - Daniel G Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Susanna Dunachie
- Oxford Centre for Global Health Research, University of Oxford, Oxford, UK
| | | | - Rachael A Evans
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Immunity and Inflammation, University of Glasgow, UK
| | - Ewen Harrison
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - J Kenneth Baillie
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK; The Pandemic Institute, University of Liverpool, UK
| | - Christopher Brightling
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, UK.
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK; The Pandemic Institute, University of Liverpool, UK.
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Green MA, Semple MG. Occupational inequalities in the prevalence of COVID-19: A longitudinal observational study of England, August 2020 to January 2021. PLoS One 2023; 18:e0283119. [PMID: 37018176 PMCID: PMC10075431 DOI: 10.1371/journal.pone.0283119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/02/2023] [Indexed: 04/06/2023] Open
Abstract
The COVID-19 pandemic has reinforced, amplified and created new health inequalities. Examining how COVID-19 prevalence varies by measures of work and occupation may help to understand these inequalities. The aim of the study is to evaluate how occupational inequalities in the prevalence of COVID-19 varies across England and their possible explanatory factors. We used data for 363,651 individuals (2,178,835 observations) aged 18 years and over between 1st May 2020 and 31st January 2021 from the Office for National Statistics Covid Infection Survey, a representative longitudinal survey of individuals in England. We focus on two measures of work; employment status for all adults, and work sector of individuals currently working. Multi-level binomial regression models were used to estimate the likelihood of testing positive of COVID-19, adjusting for known explanatory covariates. 0.9% of participants tested positive for COVID-19 over the study period. COVID-19 prevalence was higher among adults who were students or furloughed (i.e., temporarily not working). Among adults currently working, COVID-19 prevalence was highest in adults employed in the hospitality sector, with higher prevalence for individuals employed in transport, social care, retail, health care and educational sectors. Inequalities by work were not consistent over time. We find an unequal distribution of infections relating to COVID-19 by work and employment status. While our findings demonstrate the need for greater workplace interventions to protect employees tailored to their specific work sector needs, focusing on employment alone ignores the importance of SARS-CoV-2 transmission outside of employed work (i.e., furloughed and student populations).
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Affiliation(s)
- Mark A Green
- Department of Geography & Planning, University of Liverpool, Liverpool, United Kingdom
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Grundmann A, Wu C, Hardwick M, Baillie JK, Openshaw PJM, Semple MG, Böhning D, Pett S, Michael BD, Thomas RH, Galea I. Fewer COVID-19 Neurological Complications with Dexamethasone and Remdesivir. Ann Neurol 2023; 93:88-102. [PMID: 36261315 PMCID: PMC9874556 DOI: 10.1002/ana.26536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The objective of this study was to assess the impact of treatment with dexamethasone, remdesivir or both on neurological complications in acute coronavirus diease 2019 (COVID-19). METHODS We used observational data from the International Severe Acute and emerging Respiratory Infection Consortium World Health Organization (WHO) Clinical Characterization Protocol, United Kingdom. Hospital inpatients aged ≥18 years with laboratory-confirmed severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection admitted between January 31, 2020, and June 29, 2021, were included. Treatment allocation was non-blinded and performed by reporting clinicians. A propensity scoring methodology was used to minimize confounding. Treatment with remdesivir, dexamethasone, or both was assessed against the standard of care. The primary outcome was a neurological complication occurring at the point of death, discharge, or resolution of the COVID-19 clinical episode. RESULTS Out of 89,297 hospital inpatients, 64,088 had severe COVID-19 and 25,209 had non-hypoxic COVID-19. Neurological complications developed in 4.8% and 4.5%, respectively. In both groups, neurological complications were associated with increased mortality, intensive care unit (ICU) admission, worse self-care on discharge, and time to recovery. In patients with severe COVID-19, treatment with dexamethasone (n = 21,129), remdesivir (n = 1,428), and both combined (n = 10,846) were associated with a lower frequency of neurological complications: OR = 0.76 (95% confidence interval [CI] = 0.69-0.83), OR = 0.69 (95% CI = 0.51-0.90), and OR = 0.54 (95% CI = 0.47-0.61), respectively. In patients with non-hypoxic COVID-19, dexamethasone (n = 2,580) was associated with less neurological complications (OR = 0.78, 95% CI = 0.62-0.97), whereas the dexamethasone/remdesivir combination (n = 460) showed a similar trend (OR = 0.63, 95% CI = 0.31-1.15). INTERPRETATION Treatment with dexamethasone, remdesivir, or both in patients hospitalized with COVID-19 was associated with a lower frequency of neurological complications in an additive manner, such that the greatest benefit was observed in patients who received both drugs together. ANN NEUROL 2023;93:88-102.
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Affiliation(s)
- Alexander Grundmann
- Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- Department of NeurologyWessex Neurological Centre, University Hospital Southampton NHS Foundation TrustSouthamptonUK
| | - Chieh‐Hsi Wu
- Statistics, Mathematical Sciences, and Faculty of Social SciencesUniversity of SouthamptonSouthamptonUK
| | - Marc Hardwick
- Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- Department of NeurologyWessex Neurological Centre, University Hospital Southampton NHS Foundation TrustSouthamptonUK
| | - J. Kenneth Baillie
- Roslin InstituteUniversity of Edinburgh, Easter BushEdinburghUK
- Intensive Care UnitRoyal Infirmary of EdinburghEdinburghUK
| | - Peter J M Openshaw
- National Heart and Lung InstituteImperial College LondonLondonUK
- Imperial College Healthcare NHS TrustLondonUK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic InfectionsInstitute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUK
- Department of Respiratory MedicineAlder Hey Children's HospitalLiverpoolUK
| | - Dankmar Böhning
- Statistics, Mathematical Sciences, and Faculty of Social SciencesUniversity of SouthamptonSouthamptonUK
| | - Sarah Pett
- Medical Research Council Clinical Trials UnitInstitute of Clinical Trials and Methodology, University College LondonLondonUK
- Institute for Global HealthUniversity College LondonLondonUK
| | - Benedict D. Michael
- NIHR Health Protection Research Unit for Emerging and Zoonotic InfectionsInstitute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUK
- Department of Clinical Infection Microbiology and ImmunologyInstitute of Infection, Veterinary, and Ecological Sciences, University of LiverpoolLiverpoolUK
- Department of NeurologyThe Walton Centre NHS Foundation TrustLiverpoolUK
| | - Rhys H. Thomas
- Translational and Clinical Research InstituteUniversity of NewcastleNewcastle upon TyneUK
- Department of NeurologyRoyal Victoria InfirmaryNewcastle upon TyneUK
| | - Ian Galea
- Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- Department of NeurologyWessex Neurological Centre, University Hospital Southampton NHS Foundation TrustSouthamptonUK
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Green MA, Hungerford DJ, Hughes DM, Garcia-Fiñana M, Turtle L, Cheyne C, Ashton M, Leeming G, Semple MG, Singleton A, Buchan I. Changing patterns of SARS-CoV-2 infection through Delta and Omicron waves by vaccination status, previous infection and neighbourhood deprivation: a cohort analysis of 2.7 M people. BMC Infect Dis 2022; 22:889. [PMID: 36435775 PMCID: PMC9701390 DOI: 10.1186/s12879-022-07878-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/14/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Our study examines if SARS-CoV-2 infections varied by vaccination status, if an individual had previously tested positive and by neighbourhood socioeconomic deprivation across the Delta and Omicron epidemic waves of SARS-CoV-2. METHODS Population cohort study using electronic health records for 2.7 M residents in Cheshire and Merseyside, England (3rd June 2021 to 1st March 2022). Our outcome variable was registered positive test for SARS-CoV-2. Explanatory variables were vaccination status, previous registered positive test and neighbourhood socioeconomic deprivation. Cox regression models were used to analyse associations. RESULTS Originally higher SARS-CoV-2 rates in the most socioeconomically deprived neighbourhoods changed to being higher in the least deprived neighbourhoods from the 1st September 2021, and were inconsistent during the Omicron wave. Individuals who were fully vaccinated (two doses) were associated with fewer registered positive tests (e.g., individuals engaged in testing between 1st September and 27th November 2021-Hazards Ratio (HR) = 0.48, 95% Confidence Intervals (CIs) = 0.47-0.50. Individuals with a previous registered positive test were also less likely to have a registered positive test (e.g., individuals engaged in testing between 1st September and 27th November 2021-HR = 0.16, 95% CIs = 0.15-0.18. However, the Omicron period saw smaller effect sizes for both vaccination status and previous registered positive test. CONCLUSIONS Changing patterns of SARS-CoV-2 infections during the Delta and Omicron waves reveals a dynamic pandemic that continues to affect diverse communities in sometimes unexpected ways.
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Affiliation(s)
- Mark A Green
- Department of Geography and Planning, University of Liverpool, Liverpool, UK.
| | - Daniel J Hungerford
- Centre for Global Vaccine Research, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - David M Hughes
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | | | - Lance Turtle
- Centre for Global Vaccine Research, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - Christopher Cheyne
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | | | - Gary Leeming
- Civic Data Cooperative, University of Liverpool, Liverpool, UK
| | - Malcolm G Semple
- Centre for Global Vaccine Research, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alex Singleton
- Department of Geography and Planning, University of Liverpool, Liverpool, UK
| | - Iain Buchan
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, L69 7BE, UK
- Civic Data Cooperative, University of Liverpool, Liverpool, UK
- Department of Public Health and Policy, University of Liverpool, Liverpool, UK
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Swann OV, Lone NI, Harrison EM, Tomlinson LA, Walker AJ, Seaborne MJ, Pollock L, Farrell J, Hall PS, Seth S, Williams TC, Preston J, Ainsworth JS, Semple FF, Baillie JK, Katikireddi SV, Akbari A, Lyons R, Simpson CR, Semple MG, Goldacre B, Brophy S, Sheikh A, Docherty AB. Studying the Long-term Impact of COVID-19 in Kids (SLICK). Healthcare use and costs in children and young people following community-acquired SARS-CoV-2 infection: protocol for an observational study using linked primary and secondary routinely collected healthcare data from England, Scotland and Wales. BMJ Open 2022; 12:e063271. [PMID: 36356998 PMCID: PMC9659708 DOI: 10.1136/bmjopen-2022-063271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION SARS-CoV-2 infection rarely causes hospitalisation in children and young people (CYP), but mild or asymptomatic infections are common. Persistent symptoms following infection have been reported in CYP but subsequent healthcare use is unclear. We aim to describe healthcare use in CYP following community-acquired SARS-CoV-2 infection and identify those at risk of ongoing healthcare needs. METHODS AND ANALYSIS We will use anonymised individual-level, population-scale national data linking demographics, comorbidities, primary and secondary care use and mortality between 1 January 2019 and 1 May 2022. SARS-CoV-2 test data will be linked from 1 January 2020 to 1 May 2022. Analyses will use Trusted Research Environments: OpenSAFELY in England, Secure Anonymised Information Linkage (SAIL) Databank in Wales and Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 in Scotland (EAVE-II). CYP aged ≥4 and <18 years who underwent SARS-CoV-2 reverse transcription PCR (RT-PCR) testing between 1 January 2020 and 1 May 2021 and those untested CYP will be examined.The primary outcome measure is cumulative healthcare cost over 12 months following SARS-CoV-2 testing, stratified into primary or secondary care, and physical or mental healthcare. We will estimate the burden of healthcare use attributable to SARS-CoV-2 infections in the 12 months after testing using a matched cohort study of RT-PCR positive, negative or untested CYP matched on testing date, with adjustment for confounders. We will identify factors associated with higher healthcare needs in the 12 months following SARS-CoV-2 infection using an unmatched cohort of RT-PCR positive CYP. Multivariable logistic regression and machine learning approaches will identify risk factors for high healthcare use and characterise patterns of healthcare use post infection. ETHICS AND DISSEMINATION This study was approved by the South-Central Oxford C Health Research Authority Ethics Committee (13/SC/0149). Findings will be preprinted and published in peer-reviewed journals. Analysis code and code lists will be available through public GitHub repositories and OpenCodelists with meta-data via HDR-UK Innovation Gateway.
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Affiliation(s)
- Olivia V Swann
- Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
- Department of Child Life and Health, The University of Edinburgh, Edinburgh, UK
| | - Nazir I Lone
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
| | - Laurie A Tomlinson
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Alex J Walker
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Louisa Pollock
- Department of Child Health, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | - James Farrell
- Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
| | - Peter S Hall
- Institute of Cancer and Genetics, The University of Edinburgh, Edinburgh, UK
| | - Sohan Seth
- School of Informatics, The University of Edinburgh, Edinburgh, UK
| | - Thomas C Williams
- Department of Child Life and Health, The University of Edinburgh, Edinburgh, UK
| | - Jennifer Preston
- Faculty of Humanities and Social Sciences, University of Liverpool, Liverpool, UK
| | - J Samantha Ainsworth
- Faculty of Humanities and Social Sciences, University of Liverpool, Liverpool, UK
| | - Freya F Semple
- School of Medicine Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | | | | | - Ashley Akbari
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Ronan Lyons
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Colin R Simpson
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
- School of Health, Faculty of Health, Victoria University of Wellington, Wellington, New Zealand
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Respiratory Paediatrics, Alder Hey Children's Hospital, Liverpool, UK
| | - Ben Goldacre
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Sinead Brophy
- Health Data Research, Swansea University Medical School, Swansea, UK
| | - Aziz Sheikh
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
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40
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Zhou Y, Shalhoub R, Rogers SN, Yu S, Gu M, Fabre MA, Quiros PM, Shin TH, Diangson A, Deng W, Anand S, Lu W, Cullen M, Godfrey AL, Preller J, Hadjadj J, Jouanguy E, Cobat A, Abel L, Rieux-Laucat F, Terrier B, Fischer A, Novik L, Gordon IJ, Strom L, Gaudinski MR, Lisco A, Sereti I, Gniadek TJ, Biondi A, Bonfanti P, Imberti L, Dalgard CL, Zhang Y, Dobbs K, Su HC, Notarangelo LD, Wu CO, Openshaw PJ, Semple MG, Mallat Z, Baillie K, Dunbar CE, Vassiliou GS. Clonal hematopoiesis is not significantly associated with COVID-19 disease severity. Blood 2022; 140:1650-1655. [PMID: 35839449 PMCID: PMC9293387 DOI: 10.1182/blood.2022015721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yifan Zhou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Stephanie N. Rogers
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Shiqin Yu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margarete A. Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Pedro M. Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tae-Hoon Shin
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Arch Diangson
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhan Deng
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Shubha Anand
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhua Lu
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matthew Cullen
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Anna L. Godfrey
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacobus Preller
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
| | - Jerome Hadjadj
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Frederic Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Alain Fischer
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
| | - Lara Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Ingelise J. Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Larisa Strom
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Martin R. Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Andrea Lisco
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Thomas J. Gniadek
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
| | - Luisa Imberti
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Clifton L. Dalgard
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Kerry Dobbs
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - COVID-STORM Clinicians
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - NIAID Immune Response to COVID Group
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - The ISARIC4C Investigators
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Colin O. Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Peter J.M. Openshaw
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Gonçalves BP, Hall M, Jassat W, Balan V, Murthy S, Kartsonaki C, Semple MG, Rojek A, Baruch J, Reyes LF, Dasgupta A, Dunning J, Citarella BW, Pritchard M, Martín-Quiros A, Sili U, Baillie JK, Aryal D, Arabi Y, Rashan A, Angheben A, Caoili J, Carrier FM, Harrison EM, Gómez-Junyent J, Figueiredo-Mello C, Douglas JJ, Mat Nor MB, Chow YP, Wong XC, Bertagnolio S, Thwin SS, Streinu-Cercel A, Salazar L, Rishu A, Rangappa R, Ong DSY, Hashmi M, Carson G, Diaz J, Fowler R, Kraemer MUG, Wils EJ, Horby P, Merson L, Olliaro PL. An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients. eLife 2022; 11:e80556. [PMID: 36197074 PMCID: PMC9534549 DOI: 10.7554/elife.80556] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings. Methods Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries. Results Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61-0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population. Conclusions Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome. Funding Bronner P. Gonçalves, Peter Horby, Gail Carson, Piero L. Olliaro, Valeria Balan, Barbara Wanjiru Citarella, and research costs were supported by the UK Foreign, Commonwealth and Development Office (FCDO) and Wellcome [215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z]; and Janice Caoili and Madiha Hashmi were supported by the UK FCDO and Wellcome [222048/Z/20/Z]. Peter Horby, Gail Carson, Piero L. Olliaro, Kalynn Kennon and Joaquin Baruch were supported by the Bill & Melinda Gates Foundation [OPP1209135]; Laura Merson was supported by University of Oxford's COVID-19 Research Response Fund - with thanks to its donors for their philanthropic support. Matthew Hall was supported by a Li Ka Shing Foundation award to Christophe Fraser. Moritz U.G. Kraemer was supported by the Branco Weiss Fellowship, Google.org, the Oxford Martin School, the Rockefeller Foundation, and the European Union Horizon 2020 project MOOD (#874850). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Contributions from Srinivas Murthy, Asgar Rishu, Rob Fowler, James Joshua Douglas, François Martin Carrier were supported by CIHR Coronavirus Rapid Research Funding Opportunity OV2170359 and coordinated out of Sunnybrook Research Institute. Contributions from Evert-Jan Wils and David S.Y. Ong were supported by a grant from foundation Bevordering Onderzoek Franciscus; and Andrea Angheben by the Italian Ministry of Health "Fondi Ricerca corrente-L1P6" to IRCCS Ospedale Sacro Cuore-Don Calabria. The data contributions of J.Kenneth Baillie, Malcolm G. Semple, and Ewen M. Harrison were supported by grants from the National Institute for Health Research (NIHR; award CO-CIN-01), the Medical Research Council (MRC; grant MC_PC_19059), and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. All funders of the ISARIC Clinical Characterisation Group are listed in the appendix.
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Affiliation(s)
- Bronner P Gonçalves
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Waasila Jassat
- National Institute for Communicable Diseases, South Africa; Right to CareJohannesburgSouth Africa
| | - Valeria Balan
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Srinivas Murthy
- Faculty of Medicine, University of British ColumbiaVancouverCanada
| | - Christiana Kartsonaki
- MRC Population Health Research Unit, Clinical Trials Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of LiverpoolLiverpoolUnited Kingdom
- Respiratory Medicine, Alder Hey Children's Hospital, University of LiverpoolLiverpoolUnited Kingdom
| | - Amanda Rojek
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
- Royal Melbourne HospitalMelbourneAustralia
- Centre for Integrated Critical Care, University of MelbourneMelbourneAustralia
| | - Joaquín Baruch
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Luis Felipe Reyes
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
- Universidad de La SabanaChiaColombia
- Clinica Universidad de La SabanaChiaColombia
| | - Abhishek Dasgupta
- Department of Computer Science, University of OxfordOxfordUnited Kingdom
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Jake Dunning
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | | | - Mark Pritchard
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | | | - Uluhan Sili
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara UniversityIstanbulTurkey
| | - J Kenneth Baillie
- Roslin Institute, University of EdinburghEdinburghUnited Kingdom
- Intensive Care Unit, Royal Infirmary of EdinburghEdinburghUnited Kingdom
| | - Diptesh Aryal
- Critical Care and Anesthesia, Nepal Mediciti HospitalLalitpurNepal
| | - Yaseen Arabi
- King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health SciencesRiyadhSaudi Arabia
| | - Aasiyah Rashan
- Network for Improving Critical care Systems and TrainingColomboSri Lanka
| | - Andrea Angheben
- Department of Infectious, Tropical Diseases and Microbiology (DITM), IRCCS Sacro Cuore Don Calabria Hospital, Negrar di ValpolicellaVeronaItaly
| | | | - François Martin Carrier
- Department of Anesthesiology, Centre hospitalier de l'Université de MontréalMontréalCanada
- Department of Medicine, Critical Care Division, Centre hospitalier de l'Université de MontréalMontréalCanada
- Carrefour de l'innovation et santé des populations, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM)MontréalCanada
- Department of Anesthesiology and Pain Medicine, Université de MontréalMontréalCanada
| | - Ewen M Harrison
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and InformaticsEdinburghUnited Kingdom
| | - Joan Gómez-Junyent
- Department of Infectious Diseases, Hospital del Mar, Infectious Pathology and Antimicrobial Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu FabraBarcelonaSpain
| | | | | | | | - Yock Ping Chow
- Clinical Research Centre, Sunway Medical Centre, Selangor Darul EhsanSelangorMalaysia
| | - Xin Ci Wong
- Digital Health Research and Innovation Unit, Institute for Clinical Research, National Institutes of Health (NIH)SelangorMalaysia
| | | | | | - Anca Streinu-Cercel
- Carol Davila University of Medicine and PharmacyBucharestRomania
- National Institute for Infectious Diseases "Prof. Dr. Matei Bals"BucharestRomania
| | | | - Asgar Rishu
- Department of Critical Care Medicine, Sunnybrook Health Sciences CentreTorontoCanada
| | | | - David SY Ong
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & VlietlandRotterdamNetherlands
| | - Madiha Hashmi
- Critical Care Asia and Ziauddin UniversityKarachiPakistan
| | - Gail Carson
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Janet Diaz
- World Health OrganizationGenèveSwitzerland
| | - Rob Fowler
- Department of Critical Care Medicine, Sunnybrook Health Sciences CentreTorontoCanada
| | - Moritz UG Kraemer
- Department of Biology, University of OxfordOxfordUnited Kingdom
- Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Evert-Jan Wils
- Department of Intensive Care, Franciscus Gasthuis & VlietlandRotterdamNetherlands
| | - Peter Horby
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Laura Merson
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
| | - Piero L Olliaro
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
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Keeling MJ, Dyson L, Guyver-Fletcher G, Holmes A, Semple MG, Tildesley MJ, Hill EM. Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number. Stat Methods Med Res 2022; 31:1716-1737. [PMID: 35037796 PMCID: PMC9465059 DOI: 10.1177/09622802211070257] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease. Fitting mathematical models of infectious disease transmission to the available epidemiological data provide a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the effective reproduction number, [Formula: see text], has taken on special significance in terms of the general understanding of whether the epidemic is under control ([Formula: see text]). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease outbreaks. Here, focusing on the dynamics of the first wave (March-June 2020), we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the time course of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.
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Affiliation(s)
- Matt J Keeling
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, 2707University of Warwick, UK
- Joint Universities Pandemic and Epidemiological Research, https://maths.org/juniper/
| | - Louise Dyson
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, 2707University of Warwick, UK
- Joint Universities Pandemic and Epidemiological Research, https://maths.org/juniper/
| | - Glen Guyver-Fletcher
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, 2707University of Warwick, UK
- Midlands Integrative Biosciences Training Partnership, School of Life Sciences, 2707University of Warwick, UK
| | - Alex Holmes
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, 2707University of Warwick, UK
- Mathematics for Real World Systems Centre for Doctoral Training, Mathematics Institute, 2707University of Warwick, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, 4591University of Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, 4591University of Liverpool, Alder Hey Children's Hospital, Liverpool, UK
| | - Michael J Tildesley
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, 2707University of Warwick, UK
- Joint Universities Pandemic and Epidemiological Research, https://maths.org/juniper/
| | - Edward M Hill
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, 2707University of Warwick, UK
- Joint Universities Pandemic and Epidemiological Research, https://maths.org/juniper/
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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Adler H, Gould S, Hine P, Snell LB, Wong W, Houlihan CF, Osborne JC, Rampling T, Beadsworth MB, Duncan CJ, Dunning J, Fletcher TE, Hunter ER, Jacobs M, Khoo SH, Newsholme W, Porter D, Porter RJ, Ratcliffe L, Schmid ML, Semple MG, Tunbridge AJ, Wingfield T, Price NM. Clinical features and management of human monkeypox: a retrospective observational study in the UK. Lancet Infect Dis 2022; 22:1153-1162. [PMID: 35623380 PMCID: PMC9300470 DOI: 10.1016/s1473-3099(22)00228-6] [Citation(s) in RCA: 587] [Impact Index Per Article: 293.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Cases of human monkeypox are rarely seen outside of west and central Africa. There are few data regarding viral kinetics or the duration of viral shedding and no licensed treatments. Two oral drugs, brincidofovir and tecovirimat, have been approved for treatment of smallpox and have demonstrated efficacy against monkeypox in animals. Our aim was to describe the longitudinal clinical course of monkeypox in a high-income setting, coupled with viral dynamics, and any adverse events related to novel antiviral therapies. METHODS In this retrospective observational study, we report the clinical features, longitudinal virological findings, and response to off-label antivirals in seven patients with monkeypox who were diagnosed in the UK between 2018 and 2021, identified through retrospective case-note review. This study included all patients who were managed in dedicated high consequence infectious diseases (HCID) centres in Liverpool, London, and Newcastle, coordinated via a national HCID network. FINDINGS We reviewed all cases since the inception of the HCID (airborne) network between Aug 15, 2018, and Sept 10, 2021, identifying seven patients. Of the seven patients, four were men and three were women. Three acquired monkeypox in the UK: one patient was a health-care worker who acquired the virus nosocomially, and one patient who acquired the virus abroad transmitted it to an adult and child within their household cluster. Notable disease features included viraemia, prolonged monkeypox virus DNA detection in upper respiratory tract swabs, reactive low mood, and one patient had a monkeypox virus PCR-positive deep tissue abscess. Five patients spent more than 3 weeks (range 22-39 days) in isolation due to prolonged PCR positivity. Three patients were treated with brincidofovir (200 mg once a week orally), all of whom developed elevated liver enzymes resulting in cessation of therapy. One patient was treated with tecovirimat (600 mg twice daily for 2 weeks orally), experienced no adverse effects, and had a shorter duration of viral shedding and illness (10 days hospitalisation) compared with the other six patients. One patient experienced a mild relapse 6 weeks after hospital discharge. INTERPRETATION Human monkeypox poses unique challenges, even to well resourced health-care systems with HCID networks. Prolonged upper respiratory tract viral DNA shedding after skin lesion resolution challenged current infection prevention and control guidance. There is an urgent need for prospective studies of antivirals for this disease. FUNDING None.
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Affiliation(s)
- Hugh Adler
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Susan Gould
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Paul Hine
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luke B Snell
- Directorate of Infection, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Waison Wong
- Department of Paediatric Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Catherine F Houlihan
- Rare and Imported Pathogens Laboratory, UK Health Security Agency, Porton Down, Salisbury, UK; University College London, London, UK
| | - Jane C Osborne
- Rare and Imported Pathogens Laboratory, UK Health Security Agency, Porton Down, Salisbury, UK
| | - Tommy Rampling
- Rare and Imported Pathogens Laboratory, UK Health Security Agency, Porton Down, Salisbury, UK; University College London, London, UK
| | - Mike Bj Beadsworth
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Christopher Ja Duncan
- Department of Infection and Tropical Medicine, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle, UK; Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle Upon Tyne, UK
| | - Jake Dunning
- Department of Infectious Diseases, Royal Free London NHS Foundation Trust, London, UK; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; National Infection Service, UK Health Security Agency, London, UK
| | - Tom E Fletcher
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ewan R Hunter
- Department of Infection and Tropical Medicine, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Michael Jacobs
- University College London, London, UK; Department of Infectious Diseases, Royal Free London NHS Foundation Trust, London, UK
| | - Saye H Khoo
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - William Newsholme
- Directorate of Infection, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - David Porter
- Department of Paediatric Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | | | - Libuše Ratcliffe
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Matthias L Schmid
- Department of Infection and Tropical Medicine, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Malcolm G Semple
- Respiratory Unit, Alder Hey Children's NHS Foundation Trust, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anne J Tunbridge
- Department of Infectious Diseases, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield
| | - Tom Wingfield
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; World Health Organization Collaborating Centre on Tuberculosis and Social Medicine, Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - Nicholas M Price
- Directorate of Infection, Guy's & St Thomas' NHS Foundation Trust, London, UK.
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Ijaz S, Dicks S, Jegatheesan K, Parker E, Katsanovskaja K, Vink E, McClure MO, Shute J, Hope J, Cook N, Cherepanov P, Turtle L, Paxton WA, Pollakis G, Ho A, Openshaw PJM, Baillie JK, Semple MG, Tedder RS. Mapping of SARS-CoV-2 IgM and IgG in gingival crevicular fluid: Antibody dynamics and linkage to severity of COVID-19 in hospital inpatients. J Infect 2022; 85:152-160. [PMID: 35667482 PMCID: PMC9163047 DOI: 10.1016/j.jinf.2022.05.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/19/2022] [Accepted: 05/29/2022] [Indexed: 02/06/2023]
Affiliation(s)
- Samreen Ijaz
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK.
| | - Steve Dicks
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK; NHS Blood and Transplant, London, UK
| | - Keerthana Jegatheesan
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK; NHS Blood and Transplant, London, UK
| | - Eleanor Parker
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Elen Vink
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Myra O McClure
- Department of Infectious Disease, Imperial College London, London, UK
| | - J Shute
- Blood Borne Virus Unit, Reference Department, UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Joshua Hope
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Nicola Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Peter Cherepanov
- Department of Infectious Disease, Imperial College London, London, UK; Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - William A Paxton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Georgios Pollakis
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Richard S Tedder
- Department of Infectious Disease, Imperial College London, London, UK
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McNaughton AL, Paton RS, Edmans M, Youngs J, Wellens J, Phalora P, Fyfe A, Belij-Rammerstorfer S, Bolton JS, Ball J, Carnell GW, Dejnirattisai W, Dold C, Eyre DW, Hopkins P, Howarth A, Kooblall K, Klim H, Leaver S, Lee LN, López-Camacho C, Lumley SF, Macallan DC, Mentzer AJ, Provine NM, Ratcliff J, Slon-Compos J, Skelly D, Stolle L, Supasa P, Temperton N, Walker C, Wang B, Wyncoll D, Simmonds P, Lambe T, Baillie JK, Semple MG, Openshaw PJ, Obolski U, Turner M, Carroll M, Mongkolsapaya J, Screaton G, Kennedy SH, Jarvis L, Barnes E, Dunachie S, Lourenço J, Matthews PC, Bicanic T, Klenerman P, Gupta S, Thompson CP. Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses. JCI Insight 2022; 7:156372. [PMID: 35608920 PMCID: PMC9310533 DOI: 10.1172/jci.insight.156372] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
The role of immune responses to previously seen endemic coronavirus epitopes in severe acute respiratory coronavirus 2 (SARS-CoV-2) infection and disease progression has not yet been determined. Here, we show that a key characteristic of fatal outcomes with coronavirus disease 2019 (COVID-19) is that the immune response to the SARS-CoV-2 spike protein is enriched for antibodies directed against epitopes shared with endemic beta-coronaviruses and has a lower proportion of antibodies targeting the more protective variable regions of the spike. The magnitude of antibody responses to the SARS-CoV-2 full-length spike protein, its domains and subunits, and the SARS-CoV-2 nucleocapsid also correlated strongly with responses to the endemic beta-coronavirus spike proteins in individuals admitted to an intensive care unit (ICU) with fatal COVID-19 outcomes, but not in individuals with nonfatal outcomes. This correlation was found to be due to the antibody response directed at the S2 subunit of the SARS-CoV-2 spike protein, which has the highest degree of conservation between the beta-coronavirus spike proteins. Intriguingly, antibody responses to the less cross-reactive SARS-CoV-2 nucleocapsid were not significantly different in individuals who were admitted to an ICU with fatal and nonfatal outcomes, suggesting an antibody profile in individuals with fatal outcomes consistent with an "original antigenic sin" type response.
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Affiliation(s)
- Anna L. McNaughton
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Robert S. Paton
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Matthew Edmans
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jonathan Youngs
- Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - Judith Wellens
- Peter Medawar Building for Pathogen Research
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
- Translational Research for Gastrointestinal Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Prabhjeet Phalora
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Alex Fyfe
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Jai S. Bolton
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jonathan Ball
- General Intensive Care service, St George’s University Hospital National Health Service (NHS) Trust, London, United Kingdom
| | - George W. Carnell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | | | - David W. Eyre
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Philip Hopkins
- Centre for Human & Applied Physiological Sciences, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College, London, United Kingdom
| | - Alison Howarth
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kreepa Kooblall
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, and
| | - Hannah Klim
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Future of Humanity Institute, Department of Philosophy, and
| | - Susannah Leaver
- General Intensive Care service, St George’s University Hospital National Health Service (NHS) Trust, London, United Kingdom
| | - Lian Ni Lee
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | | | - Sheila F. Lumley
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derek C. Macallan
- Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | | | - Nicholas M. Provine
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jeremy Ratcliff
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Jose Slon-Compos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
| | - Donal Skelly
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Lucas Stolle
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - Chris Walker
- Meso Scale Diagnostics, Rockville, Maryland, USA
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
| | - Duncan Wyncoll
- Intensive Care Medicine, Guy’s and St Thomas’ Hospital NHS Foundation Trust, London, United Kingdom
| | | | | | - Peter Simmonds
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Teresa Lambe
- The Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom
| | | | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Uri Obolski
- School of Public Health, Faculty of Medicine, and
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Marc Turner
- National Microbiology Reference Unit, Scottish National Blood Transfusion Service, Edinburgh, United Kingdom
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
- National Infection Service, Public Health England (PHE), Salisbury, United Kingdom
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
- Siriraj Center of Research for Excellence in Dengue & Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Stephen H. Kennedy
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Lisa Jarvis
- National Microbiology Reference Unit, Scottish National Blood Transfusion Service, Edinburgh, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - José Lourenço
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Philippa C. Matthews
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tihana Bicanic
- Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Translational Research for Gastrointestinal Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Sunetra Gupta
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Craig P. Thompson
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Pazukhina E, Andreeva M, Spiridonova E, Bobkova P, Shikhaleva A, El-Taravi Y, Rumyantsev M, Gamirova A, Bairashevskaia A, Petrova P, Baimukhambetova D, Pikuza M, Abdeeva E, Filippova Y, Deunezhewa S, Nekliudov N, Bugaeva P, Bulanov N, Avdeev S, Kapustina V, Guekht A, DunnGalvin A, Comberiati P, Peroni DG, Apfelbacher C, Genuneit J, Reyes LF, Brackel CLH, Fomin V, Svistunov AA, Timashev P, Mazankova L, Miroshina A, Samitova E, Borzakova S, Bondarenko E, Korsunskiy AA, Carson G, Sigfrid L, Scott JT, Greenhawt M, Buonsenso D, Semple MG, Warner JO, Olliaro P, Needham DM, Glybochko P, Butnaru D, Osmanov IM, Munblit D, Artigas E, Avagyan A, Baziyants L, Belkina A, Berbenyuk A, Bezbabicheva T, Bezrukov V, Bordyugov S, Borisenko A, Bratukhina M, Bugaiskaya E, Chayka J, Cherdantseva Y, Degtyareva N, Druzhkova O, Dubinin A, Elifkhanova K, Eliseev D, Ezhova A, Frolova A, Ganieva J, Gorina A, Gorlenko C, Gribaleva E, Gudratova E, Ibragimova S, Kabieva K, Kalan Y, Kalinina M, Khitrina N, Kirillov B, Kiseljow H, Kislova M, Kogut N, Konova I, Korgunova M, Kotelnikova A, Kovygina K, Krupina A, Kuznetsova A, Kuznetsova A, Lavginova B, Lidjieva E, Listovskaya E, Lobova M, Loshkareva M, Lyubimova E, Mamchich D, Markina N, Maystrenko A, Mursalova A, Nagornov E, Nartova A, Nikolaeva D, Novoselov G, Ogandzhanova M, Pavlenko A, Perekosova O, Porubayeva E, Presnyakova K, Pushkareva A, Romanova O, Roshchin P, Salakhova D, Sarukhanyan I, Savina V, Shatrova J, Shishkina N, Shvedova A, Smirnov D, Solovieva V, Spasskaya O, Sukhodolskaya O, Suleimanov S, Urmantaeva N, Usalka O, Ustyan V, Valieva Y, Varaksina K, Varaksina M, Varlamova E, Vodianova M, Yegiyan M, Zaikina M, Zorina A, Zuykova E. Prevalence and risk factors of post-COVID-19 condition in adults and children at 6 and 12 months after hospital discharge: a prospective, cohort study in Moscow (StopCOVID). BMC Med 2022; 20:244. [PMID: 35794549 PMCID: PMC9257572 DOI: 10.1186/s12916-022-02448-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Previous studies assessing the prevalence of COVID-19 sequelae in adults and children were performed in the absence of an agreed definition. We investigated prevalence of post-COVID-19 condition (PCC) (WHO definition), at 6- and 12-months follow-up, amongst previously hospitalised adults and children and assessed risk factors. METHODS Prospective cohort study of children and adults with confirmed COVID-19 in Moscow, hospitalised between April and August, 2020. Two follow-up telephone interviews, using the International Severe Acute Respiratory and Emerging Infection Consortium survey, were performed at 6 and 12 months after discharge. RESULTS One thousand thirteen of 2509 (40%) of adults and 360 of 849 (42%) of children discharged participated in both the 6- and 12-month follow-ups. PCC prevalence was 50% (95% CI 47-53) in adults and 20% (95% CI 16-24) in children at 6 months, with decline to 34% (95% CI 31-37) and 11% (95% CI 8-14), respectively, at 12 months. In adults, female sex was associated with PCC at 6- and 12-month follow-up (OR 2.04, 95% CI 1.57 to 2.65) and (OR 2.04, 1.54 to 2.69), respectively. Pre-existing hypertension (OR 1.42, 1.04 to 1.94) was associated with post-COVID-19 condition at 12 months. In children, neurological comorbidities were associated with PCC both at 6 months (OR 4.38, 1.36 to 15.67) and 12 months (OR 8.96, 2.55 to 34.82) while allergic respiratory diseases were associated at 12 months (OR 2.66, 1.04 to 6.47). CONCLUSIONS Although prevalence of PCC declined one year after discharge, one in three adults and one in ten children experienced ongoing sequelae. In adults, females and persons with pre-existing hypertension, and in children, persons with neurological comorbidities or allergic respiratory diseases are at higher risk of PCC.
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Affiliation(s)
- Ekaterina Pazukhina
- Laboratory of Health Economics, Institute of Applied Economic Studies, The Russian Presidential Academy of National Economy and Public Administration, Moscow, Russia.,Center for Advanced Financial Planning, Macroeconomic Analysis and Financial Statistics, Financial Research Institute of the Ministry of Finance of the Russian Federation, Moscow, Russia
| | - Margarita Andreeva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ekaterina Spiridonova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Polina Bobkova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anastasia Shikhaleva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yasmin El-Taravi
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Mikhail Rumyantsev
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Aysylu Gamirova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anastasiia Bairashevskaia
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Polina Petrova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Dina Baimukhambetova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Maria Pikuza
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Elina Abdeeva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yulia Filippova
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Salima Deunezhewa
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Nikita Nekliudov
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Polina Bugaeva
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Nikolay Bulanov
- Tareev Clinic of Internal Diseases, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Sergey Avdeev
- Clinic of Pulmonology, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Valentina Kapustina
- Department of Internal Medicine №1, Institute of Clinical Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Alla Guekht
- Research and Clinical Center for Neuropsychiatry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Audrey DunnGalvin
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,School of Applied Psychology, University College Cork, Cork City, Ireland
| | - Pasquale Comberiati
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Diego G Peroni
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy
| | - Christian Apfelbacher
- Institute of Social Medicine and Health Systems Research, Faculty of Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jon Genuneit
- Pediatric Epidemiology, Department of Pediatrics, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Luis Felipe Reyes
- Universidad de La Sabana, Chía, Colombia.,Clínica Universidad de La Sabana, Chía, Colombia
| | - Caroline L H Brackel
- Department of Pediatric Pulmonology, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, the Netherlands.,Department of Pediatrics, Tergooi MC, Hilversum, the Netherlands
| | - Victor Fomin
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrey A Svistunov
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Peter Timashev
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Lyudmila Mazankova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Elmira Samitova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, Russia.,ZA Bashlyaeva Children's Municipal Clinical Hospital, Moscow, Russia
| | - Svetlana Borzakova
- Pirogov Russian National Research Medical University, Moscow, Russia.,Research Institute for Healthcare Organization and Medical Management of Moscow Healthcare Department, Moscow, Russia
| | - Elena Bondarenko
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anatoliy A Korsunskiy
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Gail Carson
- Nuffield Department of Medicine, ISARIC Global Support Centre, University of Oxford, Oxford, UK
| | - Louise Sigfrid
- Nuffield Department of Medicine, ISARIC Global Support Centre, University of Oxford, Oxford, UK
| | - Janet T Scott
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matthew Greenhawt
- Department of Pediatrics, Section of Allergy/Immunology, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, USA
| | - Danilo Buonsenso
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Center for Global Health Research and Studies, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.,Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - John O Warner
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Piero Olliaro
- Nuffield Department of Medicine, ISARIC Global Support Centre, University of Oxford, Oxford, UK
| | - Dale M Needham
- Outcomes After Critical Illness and Surgery (OACIS) Research Group, Johns Hopkins University, Baltimore, MD, USA.,Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Physical Medicine and Rehabilitation, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Petr Glybochko
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Denis Butnaru
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ismail M Osmanov
- Pirogov Russian National Research Medical University, Moscow, Russia.,ZA Bashlyaeva Children's Municipal Clinical Hospital, Moscow, Russia
| | - Daniel Munblit
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia. .,Research and Clinical Center for Neuropsychiatry, Moscow, Russia. .,Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK.
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Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 2022; 607:97-103. [PMID: 35255492 PMCID: PMC9259496 DOI: 10.1038/s41586-022-04576-6] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
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Affiliation(s)
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xia Shen
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine and Institute in the Park, Alder Hey Children's Hospital and University of Liverpool, Liverpool, UK
| | | | | | | | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom A Fowler
- Genomics England, London, UK
- Test and Trace, the Health Security Agency, Department of Health and Social Care, London, UK
| | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust: London, London, UK
| | | | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit and Research Centre, London, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital, London, UK
| | | | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Mark J Caulfield
- Genomics England, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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49
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Prince T, Dong X, Penrice-Randal R, Randle N, Hartley C, Goldswain H, Jones B, Semple MG, Baillie JK, Openshaw PJM, Turtle L, Hughes GL, Anderson ER, Patterson EI, Druce J, Screaton G, Carroll MW, Stewart JP, Hiscox JA. Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages. mSphere 2022; 7:e0091321. [PMID: 35491827 PMCID: PMC9241508 DOI: 10.1128/msphere.00913-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/18/2022] [Indexed: 01/02/2023] Open
Abstract
New variants of SARS-CoV-2 are continuing to emerge and dominate the global sequence landscapes. Several variants have been labeled variants of concern (VOCs) because they may have a transmission advantage, increased risk of morbidity and/or mortality, or immune evasion upon a background of prior infection or vaccination. Placing the VOCs in context with the underlying variability of SARS-CoV-2 is essential in understanding virus evolution and selection pressures. Dominant genome sequences and the population genetics of SARS-CoV-2 in nasopharyngeal swabs from hospitalized patients were characterized. Nonsynonymous changes at a minor variant level were identified. These populations were generally preserved when isolates were amplified in cell culture. To place the Alpha, Beta, Delta, and Omicron VOCs in context, their growth was compared to clinical isolates of different lineages from earlier in the pandemic. The data indicated that the growth in cell culture of the Beta variant was more than that of the other variants in Vero E6 cells but not in hACE2-A549 cells. Looking at each time point, Beta grew more than the other VOCs in hACE2-A549 cells at 24 to 48 h postinfection. At 72 h postinfection there was no difference in the growth of any of the variants in either cell line. Overall, this work suggested that exploring the biology of SARS-CoV-2 is complicated by population dynamics and that these need to be considered with new variants. In the context of variation seen in other coronaviruses, the variants currently observed for SARS-CoV-2 are very similar in terms of their clinical spectrum of disease. IMPORTANCE SARS-CoV-2 is the causative agent of COVID-19. The virus has spread across the planet, causing a global pandemic. In common with other coronaviruses, SARS-CoV-2 genomes can become quite diverse as a consequence of replicating inside cells. This has given rise to multiple variants from the original virus that infected humans. These variants may have different properties and in the context of a widespread vaccination program may render vaccines less effective. Our research confirms the degree of genetic diversity of SARS-CoV-2 in patients. By comparing the growth of previous variants to the pattern seen with four variants of concern (VOCs) (Alpha, Beta, Delta, and Omicron), we show that, at least in cells, Beta variant growth exceeds that of Alpha, Delta, and Omicron VOCs at 24 to 48 h in both Vero E6 and hACE2-A549 cells, but by 72 h postinfection, the amount of virus is not different from that of the other VOCs.
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Affiliation(s)
- Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nadine Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Benjamin Jones
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Malcolm G. Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Department of Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - J. Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Enyia R. Anderson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edward I. Patterson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Julian Druce
- Virus Identification Laboratory, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Gavin Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Miles W. Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Public Health England, Salisbury, United Kingdom
| | - James P. Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Infectious Disease, University of Georgia, Georgia, USA
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
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50
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Knight GM, Pham TM, Stimson J, Funk S, Jafari Y, Pople D, Evans S, Yin M, Brown CS, Bhattacharya A, Hope R, Semple MG, Read JM, Cooper BS, Robotham JV. The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020. BMC Infect Dis 2022; 22:556. [PMID: 35717168 PMCID: PMC9206097 DOI: 10.1186/s12879-022-07490-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 05/25/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND SARS-CoV-2 is known to transmit in hospital settings, but the contribution of infections acquired in hospitals to the epidemic at a national scale is unknown. METHODS We used comprehensive national English datasets to determine the number of COVID-19 patients with identified hospital-acquired infections (with symptom onset > 7 days after admission and before discharge) in acute English hospitals up to August 2020. As patients may leave the hospital prior to detection of infection or have rapid symptom onset, we combined measures of the length of stay and the incubation period distribution to estimate how many hospital-acquired infections may have been missed. We used simulations to estimate the total number (identified and unidentified) of symptomatic hospital-acquired infections, as well as infections due to onward community transmission from missed hospital-acquired infections, to 31st July 2020. RESULTS In our dataset of hospitalised COVID-19 patients in acute English hospitals with a recorded symptom onset date (n = 65,028), 7% were classified as hospital-acquired. We estimated that only 30% (range across weeks and 200 simulations: 20-41%) of symptomatic hospital-acquired infections would be identified, with up to 15% (mean, 95% range over 200 simulations: 14.1-15.8%) of cases currently classified as community-acquired COVID-19 potentially linked to hospital transmission. We estimated that 26,600 (25,900 to 27,700) individuals acquired a symptomatic SARS-CoV-2 infection in an acute Trust in England before 31st July 2020, resulting in 15,900 (15,200-16,400) or 20.1% (19.2-20.7%) of all identified hospitalised COVID-19 cases. CONCLUSIONS Transmission of SARS-CoV-2 to hospitalised patients likely caused approximately a fifth of identified cases of hospitalised COVID-19 in the "first wave" in England, but less than 1% of all infections in England. Using time to symptom onset from admission for inpatients as a detection method likely misses a substantial proportion (> 60%) of hospital-acquired infections.
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Affiliation(s)
- Gwenan M Knight
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Thi Mui Pham
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - James Stimson
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, Colindale, London, UK
| | - Sebastian Funk
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Yalda Jafari
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Diane Pople
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, Colindale, London, UK
| | - Stephanie Evans
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, Colindale, London, UK
| | - Mo Yin
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- National University of Singapore Department of Medicine, Singapore, Singapore
| | - Colin S Brown
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, Colindale, London, UK
| | - Alex Bhattacharya
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, Colindale, London, UK
| | - Russell Hope
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, Colindale, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Jonathan M Read
- Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Ben S Cooper
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Julie V Robotham
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, Colindale, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in Partnership with PHE, Oxford, UK
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